Notebook

Black Abalone Digestive Gland Transcriptome Annotation¶

Blast output from de novo assembly of Carmel Exposed and Control Libraries

In [1]:

#tab-delited fasta
!date

Wed Mar  5 11:16:17 PST 2014

fasta: http://eagle.fish.washington.edu/cnidarian/BlackAbalone_Contigs_v3.fa

In [2]:

!head /Volumes/web/cnidarian/BlackAbalone_Contigs_v3.fa

>Roberts_20100712_CC_F3_trimmed_contig_1 Average coverage: 38.44
ATTTAAAGTGTTTGATAAAGACAATAACGGCTTCATCAGTAAATCCGAGCTCCGGCAGGT
CATGGTGTCTTTGGAGGGTCACAAGGTCACCGAGCAGGAAATCAGCGAC
>Roberts_20100712_CC_F3_trimmed_contig_2 Average coverage: 153.77
CTTCAGCACAACTCAGGTGTCTGTCCGGCCGTTACAGCACACCCAGTTTGAGCGGTTCAT
CCCTGCAGCCTACCCATATTACACCAGTGCCTTCTCCATGATGTTTGGAGTCCTTATACT
GAGTATAGTGTTCTCATGCCCTGTCCTTCTTGGATTCC
>Roberts_20100712_CC_F3_trimmed_contig_3 Average coverage: 175.58
TGGAGGTGGGGTGCCTCATAGATGGTTTGGACTTGCCGGTCCTATAGGAGCAGGGGAATG
GGGAAACCCAAGGTCGAGCTACCTGACACACGCCTTGGCCG

In [3]:

!sed 's/Roberts_20100712_CC_F3_trimmed_/BlackAbalone_v3_/g' </Volumes/web/cnidarian/BlackAbalone_Contigs_v3.fa> /Volumes/web/cnidarian/lft_BlackAbalone_v3_fasta.fa
#sed 's/abc/XYZ/g' <infile >outfile

In [6]:

!head /Volumes/web/cnidarian/lft_BlackAbalone_v3_fasta.fa

>BlackAbalone_v3_contig_1 Average coverage: 38.44
ATTTAAAGTGTTTGATAAAGACAATAACGGCTTCATCAGTAAATCCGAGCTCCGGCAGGT
CATGGTGTCTTTGGAGGGTCACAAGGTCACCGAGCAGGAAATCAGCGAC
>BlackAbalone_v3_contig_2 Average coverage: 153.77
CTTCAGCACAACTCAGGTGTCTGTCCGGCCGTTACAGCACACCCAGTTTGAGCGGTTCAT
CCCTGCAGCCTACCCATATTACACCAGTGCCTTCTCCATGATGTTTGGAGTCCTTATACT
GAGTATAGTGTTCTCATGCCCTGTCCTTCTTGGATTCC
>BlackAbalone_v3_contig_3 Average coverage: 175.58
TGGAGGTGGGGTGCCTCATAGATGGTTTGGACTTGCCGGTCCTATAGGAGCAGGGGAATG
GGGAAACCCAAGGTCGAGCTACCTGACACACGCCTTGGCCG

In [7]:

!grep -c ">" /Volumes/web/cnidarian/lft_BlackAbalone_v3_fasta.fa

Details of assembly in CLC

Generic Annotation¶

code
./blastx -query /Volumes/web-1/cnidarian/BlackAbalone_Contigs_v3.fa -db /Volumes/web-1/whale/fish546/blast/db/swissprot -out /Volumes/web-1/cnidarian/lft_BlackAbalone_v3_swissprot_blastout -outfmt 6 -evalue 1E-5 -max_target_seqs 1 -num_threads 4

In [5]:

!head /Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout

Roberts_20100712_CC_F3_trimmed_contig_1	gi|41018621|sp|P60204.2|CALM_EMENI	64.71	34	11	1	2	103	90	122	6e-08	48.5
Roberts_20100712_CC_F3_trimmed_contig_2	gi|218546747|sp|B1H3C9.1|OST48_XENTR	81.82	44	8	0	2	133	384	427	5e-18	79.7
Roberts_20100712_CC_F3_trimmed_contig_6	gi|133940|sp|P02350.2|RS31_XENLA	100.00	57	0	0	1	171	10	66	4e-32	 115
Roberts_20100712_CC_F3_trimmed_contig_7	gi|21362398|sp|P70097.1|C560_CRIGR	46.76	139	70	2	7	414	3	140	9e-29	 108
Roberts_20100712_CC_F3_trimmed_contig_9	gi|302393789|sp|P62972.2|UBIQP_XENLA	100.00	69	0	0	2	208	8	76	9e-42	 139
Roberts_20100712_CC_F3_trimmed_contig_15	gi|74851961|sp|Q54GK6.1|RL222_DICDI	59.46	37	15	0	2	112	45	81	7e-08	48.1
Roberts_20100712_CC_F3_trimmed_contig_19	gi|231498|sp|P30163.1|ACT2_ONCVO	98.08	260	5	0	1	780	32	291	0.0	 537
Roberts_20100712_CC_F3_trimmed_contig_22	gi|158706130|sp|Q08CS6.2|MOXD2_DANRE	33.73	83	51	2	1	237	448	530	1e-08	54.7
Roberts_20100712_CC_F3_trimmed_contig_26	gi|6226551|sp|P29957.3|AMY_PSEHA	50.98	51	21	1	1	153	527	573	9e-08	51.2
Roberts_20100712_CC_F3_trimmed_contig_28	gi|133802|sp|P20342.3|RS15_XENLA	100.00	44	0	0	3	134	102	145	5e-25	95.1

In [7]:

!tail /Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout

Roberts_20100712_CC_F3_trimmed_contig_13606	gi|48474943|sp|Q99NF1.1|BCDO2_MOUSE	60.00	30	12	0	2	91	226	255	3e-06	45.8
Roberts_20100712_CC_F3_trimmed_contig_13614	gi|82179554|sp|Q5M9A7.1|PGAP2_XENLA	68.29	41	13	0	2	124	60	100	2e-14	67.0
Roberts_20100712_CC_F3_trimmed_contig_13615	gi|158957572|sp|Q0P457.2|KTI12_DANRE	68.57	35	11	0	3	107	239	273	2e-10	56.6
Roberts_20100712_CC_F3_trimmed_contig_13618	gi|46577124|sp|Q9H3K6.1|BOLA2_HUMAN	60.00	35	14	0	3	107	52	86	2e-09	52.8
Roberts_20100712_CC_F3_trimmed_contig_13654	gi|2493067|sp|Q36967.1|ATP6_SALTR	95.12	41	2	0	3	125	2	42	1e-18	76.6
Roberts_20100712_CC_F3_trimmed_contig_13686	gi|66774221|sp|Q9CZR2.2|NALD2_MOUSE	60.61	33	13	0	6	104	670	702	3e-07	49.3
Roberts_20100712_CC_F3_trimmed_contig_13693	gi|71153494|sp|Q9H583.3|HEAT1_HUMAN	47.73	44	23	0	5	136	1991	2034	2e-06	47.4
Roberts_20100712_CC_F3_trimmed_contig_13748	gi|122136056|sp|Q2KIM0.1|FUCO_BOVIN	55.56	36	16	0	6	113	202	237	7e-08	50.4
Roberts_20100712_CC_F3_trimmed_contig_13845	gi|229462816|sp|Q9UKP5.2|ATS6_HUMAN	39.29	84	44	3	46	297	556	632	3e-09	57.4
Roberts_20100712_CC_F3_trimmed_contig_13882	gi|166217735|sp|A1USB4.1|GATB_BARBK	61.29	31	12	0	10	102	12	42	1e-06	47.0

In [6]:

!grep -c "Roberts" /Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout

In [28]:

#now with version28
!blastx -query /Volumes/web/cnidarian/BlackAbalone_Contigs_v3.fa -db /Volumes/web/whale/fish546/blast/db/swissprot -out /Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout_tax1 -outfmt "6 std stitle staxids sscinames scomnames sblastnames" -evalue 1E-10 -max_target_seqs 1 

Selenocysteine (U) at position 613 replaced by X
Selenocysteine (U) at position 613 replaced by X
Selenocysteine (U) at position 24 replaced by X
Selenocysteine (U) at position 63 replaced by X
Selenocysteine (U) at position 25 replaced by X
Selenocysteine (U) at position 63 replaced by X
Selenocysteine (U) at position 60 replaced by X
Selenocysteine (U) at position 73 replaced by X
Selenocysteine (U) at position 73 replaced by X
Selenocysteine (U) at position 73 replaced by X
Selenocysteine (U) at position 73 replaced by X
Selenocysteine (U) at position 73 replaced by X
Selenocysteine (U) at position 73 replaced by X
Selenocysteine (U) at position 73 replaced by X
Selenocysteine (U) at position 73 replaced by X
Selenocysteine (U) at position 73 replaced by X
Selenocysteine (U) at position 64 replaced by X

In [ ]:

#Updating July 24, 2013
#Want to GOslim pie the transcriptome based on Swiss-Prot
#tr ',' "\t"

In [9]:

!tr '|' "\t" </Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout> /Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout_b

In [10]:

!head /Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout_b

Roberts_20100712_CC_F3_trimmed_contig_1	gi	41018621	sp	P60204.2	CALM_EMENI	64.71	34	11	1	2	103	90	122	6e-08	48.5
Roberts_20100712_CC_F3_trimmed_contig_2	gi	218546747	sp	B1H3C9.1	OST48_XENTR	81.82	44	8	0	2	133	384	427	5e-18	79.7
Roberts_20100712_CC_F3_trimmed_contig_6	gi	133940	sp	P02350.2	RS31_XENLA	100.00	57	0	0	1	171	10	66	4e-32	 115
Roberts_20100712_CC_F3_trimmed_contig_7	gi	21362398	sp	P70097.1	C560_CRIGR	46.76	139	70	2	7	414	3	140	9e-29	 108
Roberts_20100712_CC_F3_trimmed_contig_9	gi	302393789	sp	P62972.2	UBIQP_XENLA	100.00	69	0	0	2	208	8	76	9e-42	 139
Roberts_20100712_CC_F3_trimmed_contig_15	gi	74851961	sp	Q54GK6.1	RL222_DICDI	59.46	37	15	0	2	112	45	81	7e-08	48.1
Roberts_20100712_CC_F3_trimmed_contig_19	gi	231498	sp	P30163.1	ACT2_ONCVO	98.08	260	5	0	1	780	32	291	0.0	 537
Roberts_20100712_CC_F3_trimmed_contig_22	gi	158706130	sp	Q08CS6.2	MOXD2_DANRE	33.73	83	51	2	1	237	448	530	1e-08	54.7
Roberts_20100712_CC_F3_trimmed_contig_26	gi	6226551	sp	P29957.3	AMY_PSEHA	50.98	51	21	1	1	153	527	573	9e-08	51.2
Roberts_20100712_CC_F3_trimmed_contig_28	gi	133802	sp	P20342.3	RS15_XENLA	100.00	44	0	0	3	134	102	145	5e-25	95.1

In [11]:

#also need to get rid of version # on Swiss-Prot ID
#note that it will also break bitscore 
!tr '.' "\t" </Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout_b> /Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout_c

In [12]:

!head /Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout_c

Roberts_20100712_CC_F3_trimmed_contig_1	gi	41018621	sp	P60204	2	CALM_EMENI	64	71	34	11	1	2	103	90	122	6e-08	48	5
Roberts_20100712_CC_F3_trimmed_contig_2	gi	218546747	sp	B1H3C9	1	OST48_XENTR	81	82	44	8	0	2	133	384	427	5e-18	79	7
Roberts_20100712_CC_F3_trimmed_contig_6	gi	133940	sp	P02350	2	RS31_XENLA	100	00	57	0	0	1	171	10	66	4e-32	 115
Roberts_20100712_CC_F3_trimmed_contig_7	gi	21362398	sp	P70097	1	C560_CRIGR	46	76	139	70	2	7	414	3	140	9e-29	 108
Roberts_20100712_CC_F3_trimmed_contig_9	gi	302393789	sp	P62972	2	UBIQP_XENLA	100	00	69	0	0	2	208	8	76	9e-42	 139
Roberts_20100712_CC_F3_trimmed_contig_15	gi	74851961	sp	Q54GK6	1	RL222_DICDI	59	46	37	15	0	2	112	45	81	7e-08	48	1
Roberts_20100712_CC_F3_trimmed_contig_19	gi	231498	sp	P30163	1	ACT2_ONCVO	98	08	260	5	0	1	780	32	291	0	0	 537
Roberts_20100712_CC_F3_trimmed_contig_22	gi	158706130	sp	Q08CS6	2	MOXD2_DANRE	33	73	83	51	2	1	237	448	530	1e-08	54	7
Roberts_20100712_CC_F3_trimmed_contig_26	gi	6226551	sp	P29957	3	AMY_PSEHA	50	98	51	21	1	1	153	527	573	9e-08	51	2
Roberts_20100712_CC_F3_trimmed_contig_28	gi	133802	sp	P20342	3	RS15_XENLA	100	00	44	0	0	3	134	102	145	5e-25	95	1

In [32]:

!sed 's/Roberts_20100712_CC_F3_trimmed/Haliotis_cra_v3/g' </Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout_c> /Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout_d
#sed 's/abc/XYZ/g' <infile >outfile

In [33]:

!head /Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout_d

Haliotis_cra_v3_contig_1	gi	41018621	sp	P60204	2	CALM_EMENI	64	71	34	11	1	2	103	90	122	6e-08	48	5
Haliotis_cra_v3_contig_2	gi	218546747	sp	B1H3C9	1	OST48_XENTR	81	82	44	8	0	2	133	384	427	5e-18	79	7
Haliotis_cra_v3_contig_6	gi	133940	sp	P02350	2	RS31_XENLA	100	00	57	0	0	1	171	10	66	4e-32	 115
Haliotis_cra_v3_contig_7	gi	21362398	sp	P70097	1	C560_CRIGR	46	76	139	70	2	7	414	3	140	9e-29	 108
Haliotis_cra_v3_contig_9	gi	302393789	sp	P62972	2	UBIQP_XENLA	100	00	69	0	0	2	208	8	76	9e-42	 139
Haliotis_cra_v3_contig_15	gi	74851961	sp	Q54GK6	1	RL222_DICDI	59	46	37	15	0	2	112	45	81	7e-08	48	1
Haliotis_cra_v3_contig_19	gi	231498	sp	P30163	1	ACT2_ONCVO	98	08	260	5	0	1	780	32	291	0	0	 537
Haliotis_cra_v3_contig_22	gi	158706130	sp	Q08CS6	2	MOXD2_DANRE	33	73	83	51	2	1	237	448	530	1e-08	54	7
Haliotis_cra_v3_contig_26	gi	6226551	sp	P29957	3	AMY_PSEHA	50	98	51	21	1	1	153	527	573	9e-08	51	2
Haliotis_cra_v3_contig_28	gi	133802	sp	P20342	3	RS15_XENLA	100	00	44	0	0	3	134	102	145	5e-25	95	1

In [15]:

!wc /Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout_d

    1842   34752  186913 /Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout_d

In [14]:

#lets try again to see if can commandline up to SQLShare
!cd /Users/sr320/pythonclient/tools

In [25]:

#cp samtools /usr/local/bin
!cp uploadone.py /usr/local/bin

cp: /usr/local/bin: Permission denied

In [ ]:

#SQLShare direct.

Update: Joining Blast with more info¶

In [7]:

!python /Users/sr320/sqlshare-pythonclient/tools/fetchdata.py -d "[sr320@washington.edu].[lft_BlackAbalone_v3_SP_GO_pathway]" -f tsv -o /Volumes/web/cnidarian/lft_BlackAbalone_sp_go_path.txt

https://sqlshare.escience.washington.edu/sqlshare/#s=query%2Fsr320%2540washington.edu%2Flft_BlackAbalone_v3_SP_GO_pathway&q=

In [9]:

!head -2 /Volumes/web/cnidarian/lft_BlackAbalone_sp_go_path.txt

In [10]:

!wc /Volumes/web/cnidarian/lft_BlackAbalone_sp_go_path.txt

    1843   96683  938139 /Volumes/web/cnidarian/lft_BlackAbalone_sp_go_path.txt

http://eagle.fish.washington.edu/cnidarian/lft_BlackAbalone_sp_go_path.txt

SQLShare Joining¶

Input: https://sqlshare.escience.washington.edu/sqlshare#s=query/sr320%40washington.edu/lft_BlackAbalone_v3_swissprot_blastout_d

  SELECT distinct * 
  FROM [sr320@washington.edu].[lft_BlackAbalone_v3_swissprot_blastout_d]d
  left join
  [sr320@washington.edu].[SPID and GO Numbers]go
  on
  d.SPID = go.SPID

adding Slim info...

  SELECT distinct * 
  FROM [sr320@washington.edu].[lft_BlackAbalone_v3_swissprot_blastout_d]d
  left join
  [sr320@washington.edu].[SPID and GO Numbers]go
  on
  d.SPID = go.SPID
  left join 
  [sr320@washington.edu].[GO_to_GOslim]slim
  on 
  go.GOID = slim.GO_id

https://sqlshare.escience.washington.edu/sqlshare#s=query/sr320%40washington.edu/lft_BlackAbalone_v3_GO

To get GO Slim info

  SELECT Distinct
  ContigID,
  GOSlim_bin,
  evalue
  FROM [sr320@washington.edu].[lft_BlackAbalone_v3_GO]
  Where aspect like 'P'

might should consider thresholding evalue

SELECT Distinct
  ContigID,
  GOSlim_bin,
  evalue
  FROM [sr320@washington.edu].[lft_BlackAbalone_v3_GO]
  Where aspect like 'P'
  and 
  evalue < 1E-10

In [3]:

!head /Volumes/web/cnidarian/lft_BlackAbalone_v3GOslim.csv

In [10]:

!wc /Volumes/web/cnidarian/lft_BlackAbalone_v3GOslim.csv

    2352    5731  133085 /Volumes/web/cnidarian/lft_BlackAbalone_v3GOslim.csv

In [11]:

#query with no evalue limit to verify accuracy
!head /Volumes/web/cnidarian/lft_BlackAbalone_v3GOslim_jp.csv

In [12]:

!wc /Volumes/web/cnidarian/lft_BlackAbalone_v3GOslim_jp.csv

    3430    8417  194682 /Volumes/web/cnidarian/lft_BlackAbalone_v3GOslim_jp.csv

wwcd - (verified again in exhell)

In [4]:

#will try the R
%pylab inline

Welcome to pylab, a matplotlib-based Python environment [backend: module://IPython.zmq.pylab.backend_inline].
For more information, type 'help(pylab)'.

In [5]:

import numpy as np
import matplotlib.pylab as plt

In [7]:

import rpy2

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-7-2dcec3d9bd52> in <module>()
----> 1 import rpy2

ImportError: No module named rpy2

Gave up and used EXCEL

iPath¶

getting data into format

SELECT Distinct
  ContigID,
  SPID
  FROM [sr320@washington.edu].[lft_BlackAbalone_v3_GO]
  Where 
  evalue < 1E-10

1210 IDs

http://eagle.fish.washington.edu/cnidarian/BlackAb_ipath.svg

code ./blastx -query /Volumes/web-1/cnidarian/BlackAbalone_Contigs_v3.fa -db /Volumes/web-1/whale/fish546/blast/db/nr -out /Volumes/web-1/cnidarian/lft_BlackAbalone_v3_nr_blastout -outfmt 6 -evalue 1E-5 -max_target_seqs 1 -num_threads 4

In [8]:

!head /Volumes/web/cnidarian/lft_BlackAbalone_v3_nr_blastout

Roberts_20100712_CC_F3_trimmed_contig_1	gi|166714376|gb|ABY87953.1|	67.65	34	10	1	2	103	90	122	7e-07	49.7
Roberts_20100712_CC_F3_trimmed_contig_2	gi|109020229|ref|XP_001111903.1|	81.82	44	8	0	2	133	72	115	1e-17	79.3
Roberts_20100712_CC_F3_trimmed_contig_6	gi|149068841|gb|EDM18393.1|	100.00	57	0	0	1	171	10	66	4e-32	 116
Roberts_20100712_CC_F3_trimmed_contig_7	gi|169153945|emb|CAQ14310.1|	48.94	141	67	2	4	414	1	140	4e-34	 127
Roberts_20100712_CC_F3_trimmed_contig_9	gi|342326368|gb|AEL23099.1|	100.00	69	0	0	2	208	15	83	3e-41	 140
Roberts_20100712_CC_F3_trimmed_contig_10	gi|166406892|gb|ABY87409.1|	75.76	33	8	0	6	104	43	75	4e-09	56.2
Roberts_20100712_CC_F3_trimmed_contig_14	gi|91992330|gb|ABE72920.1|	96.43	56	2	0	43	210	371	426	2e-30	 120
Roberts_20100712_CC_F3_trimmed_contig_15	gi|340382506|ref|XP_003389760.1|	72.97	37	10	0	2	112	56	92	6e-09	55.5
Roberts_20100712_CC_F3_trimmed_contig_17	gi|340370586|ref|XP_003383827.1|	60.53	38	15	0	1	114	218	255	5e-12	65.5
Roberts_20100712_CC_F3_trimmed_contig_19	gi|37528876|gb|AAQ92368.1|	99.62	260	1	0	1	780	32	291	0.0	 542

In [9]:

!tail /Volumes/web/cnidarian/lft_BlackAbalone_v3_nr_blastout

Roberts_20100712_CC_F3_trimmed_contig_13618	gi|348544575|ref|XP_003459756.1|	71.43	35	10	0	3	107	73	107	8e-10	58.2
Roberts_20100712_CC_F3_trimmed_contig_13654	gi|62240178|gb|AAX77257.1|	100.00	41	0	0	3	125	120	160	8e-19	83.6
Roberts_20100712_CC_F3_trimmed_contig_13686	gi|340384210|ref|XP_003390607.1|	66.67	33	11	0	6	104	700	732	1e-07	55.1
Roberts_20100712_CC_F3_trimmed_contig_13693	gi|115767231|ref|XP_782598.2|	59.09	44	18	0	5	136	1316	1359	8e-09	58.9
Roberts_20100712_CC_F3_trimmed_contig_13748	gi|328793281|ref|XP_395852.4|	75.00	36	9	0	6	113	209	244	7e-10	60.8
Roberts_20100712_CC_F3_trimmed_contig_13760	gi|32407325|gb|AAP41556.1|	93.33	30	2	0	2	91	299	328	3e-07	53.1
Roberts_20100712_CC_F3_trimmed_contig_13804	gi|166406789|gb|ABY87358.1|	70.45	44	13	0	2	133	239	282	3e-14	73.6
Roberts_20100712_CC_F3_trimmed_contig_13845	gi|156378102|ref|XP_001630983.1|	54.69	64	22	3	49	240	58	114	6e-09	57.8
Roberts_20100712_CC_F3_trimmed_contig_13855	gi|261754259|ref|ZP_05997968.1|	80.49	41	8	0	123	1	14	54	2e-15	72.0
Roberts_20100712_CC_F3_trimmed_contig_13882	gi|144899095|emb|CAM75959.1|	66.67	30	10	0	13	102	1	30	1e-05	48.9

In [10]:

!grep -c "Roberts" /Volumes/web/cnidarian/lft_BlackAbalone_v3_nr_blastout

code ./blastn -query /Volumes/web-1/cnidarian/BlackAbalone_Contigs_v3.fa -db /Volumes/CLC_blastdatabases/nt -out /Volumes/web-1/cnidarian/lft_BlackAbalone_v3_nt_blastout -outfmt 6 -evalue 1E-5 -max_target_seqs 1 -num_threads 6 -task blastn

In [17]:

!head /Volumes/web/cnidarian/lft_BlackAbalone_v3_nt_blastout

Roberts_20100712_CC_F3_trimmed_contig_2	gi|115947556|ref|XM_796732.2|	84.21	114	18	0	2	115	605	718	7e-26	 125
Roberts_20100712_CC_F3_trimmed_contig_4	gi|177667010|gb|EU595789.1|	85.97	221	31	0	3	223	9228	9008	8e-66	 259
Roberts_20100712_CC_F3_trimmed_contig_6	gi|345329379|ref|XM_001506155.2|	86.96	161	21	0	1	161	60	220	5e-47	 196
Roberts_20100712_CC_F3_trimmed_contig_9	gi|306922143|dbj|AB490993.1|	88.67	203	23	0	5	207	364	566	6e-67	 262
Roberts_20100712_CC_F3_trimmed_contig_10	gi|166406891|gb|EU244393.1|	80.85	94	18	0	12	105	133	226	4e-15	89.7
Roberts_20100712_CC_F3_trimmed_contig_14	gi|91992331|gb|DQ453716.1|	97.65	213	5	0	1	213	955	1167	1e-96	 361
Roberts_20100712_CC_F3_trimmed_contig_15	gi|345492297|ref|XM_001600219.2|	75.89	112	27	0	1	112	225	336	2e-12	80.6
Roberts_20100712_CC_F3_trimmed_contig_17	gi|260831083|ref|XM_002610443.1|	86.27	51	7	0	37	87	762	812	2e-06	60.8
Roberts_20100712_CC_F3_trimmed_contig_19	gi|270313645|gb|GU263793.1|	99.10	782	7	0	1	782	164	945	0.0	1379
Roberts_20100712_CC_F3_trimmed_contig_20	gi|89331166|dbj|AB234872.1|	95.93	369	15	0	1	369	544	912	1e-167	 598

In [19]:

!tail /Volumes/web/cnidarian/lft_BlackAbalone_v3_nt_blastout

Roberts_20100712_CC_F3_trimmed_contig_13802	gi|300386193|gb|GU995619.1|	81.36	118	21	1	7	124	422	538	1e-21	 111
Roberts_20100712_CC_F3_trimmed_contig_13804	gi|166406788|gb|EU244341.1|	81.95	133	24	0	1	133	716	848	4e-28	 132
Roberts_20100712_CC_F3_trimmed_contig_13813	gi|300385867|gb|GU995293.1|	87.30	63	5	2	3	63	229	290	9e-10	71.6
Roberts_20100712_CC_F3_trimmed_contig_13820	gi|356473005|gb|HQ650445.1|	88.89	54	6	0	1	54	54	107	8e-10	71.6
Roberts_20100712_CC_F3_trimmed_contig_13828	gi|60219427|emb|CR388147.13|	83.61	61	6	2	95	155	89790	89734	2e-06	60.8
Roberts_20100712_CC_F3_trimmed_contig_13855	gi|3930574|gb|AF069062.1|AF069062	99.23	130	1	0	1	130	289	418	2e-57	 230
Roberts_20100712_CC_F3_trimmed_contig_13858	gi|13195722|gb|AF133090.2|AF133090	100.00	115	0	0	1	115	73	187	5e-51	 208
Roberts_20100712_CC_F3_trimmed_contig_13860	gi|190356750|emb|AM999887.1|	84.09	132	19	2	1	131	1236811	1236941	3e-29	 136
Roberts_20100712_CC_F3_trimmed_contig_13863	gi|82541884|gb|DQ291132.1|	87.76	49	6	0	13	61	102093	102045	5e-07	62.6
Roberts_20100712_CC_F3_trimmed_contig_13871	gi|13195722|gb|AF133090.2|AF133090	100.00	91	0	0	1	91	547	637	5e-38	 165

In [20]:

!grep -c "Roberts" /Volumes/web/cnidarian/lft_BlackAbalone_v3_nt_blastout

Attempt to get taxonomy information using blast version 2.2.28¶

./blastn -query /Volumes/web-1/cnidarian/BlackAbalone_Contigs_v3.fa -db /Volumes/CLC_blastdatabases/nt -out /Volumes/web-1/cnidarian/lft_BlackAbalone_v3_nt_blastout_taxa1 -outfmt "6 qseqid sseqid sallseqid pident length evalue bitscore staxids sscinames scomnames sblastnames qcovs" -evalue 1E-5 -max_target_seqs 1 -num_threads 10 -task blastn

without luck

In [21]:

!head /Volumes/web/cnidarian/lft_BlackAbalone_v3_nt_blastout_taxa1

Roberts_20100712_CC_F3_trimmed_contig_2	gi|115947556|ref|XM_796732.2|	gi|115947556|ref|XM_796732.2|	84.21	114	7e-26	 125	7668	N/A	N/A	N/A	72
Roberts_20100712_CC_F3_trimmed_contig_4	gi|177667010|gb|EU595789.1|	gi|177667010|gb|EU595789.1|	85.97	221	8e-66	 259	42344	N/A	N/A	N/A	93
Roberts_20100712_CC_F3_trimmed_contig_6	gi|345329379|ref|XM_001506155.2|	gi|345329379|ref|XM_001506155.2|	86.96	161	5e-47	 196	9258	N/A	N/A	N/A	93
Roberts_20100712_CC_F3_trimmed_contig_9	gi|306922143|dbj|AB490993.1|	gi|306922143|dbj|AB490993.1|	88.67	203	6e-67	 262	214486	N/A	N/A	N/A	89
Roberts_20100712_CC_F3_trimmed_contig_9	gi|306922143|dbj|AB490993.1|	gi|306922143|dbj|AB490993.1|	87.25	204	1e-62	 248	214486	N/A	N/A	N/A	89
Roberts_20100712_CC_F3_trimmed_contig_9	gi|306922143|dbj|AB490993.1|	gi|306922143|dbj|AB490993.1|	85.71	203	9e-59	 235	214486	N/A	N/A	N/A	89
Roberts_20100712_CC_F3_trimmed_contig_9	gi|306922143|dbj|AB490993.1|	gi|306922143|dbj|AB490993.1|	90.00	110	1e-32	 149	214486	N/A	N/A	N/A	89
Roberts_20100712_CC_F3_trimmed_contig_10	gi|166406891|gb|EU244393.1|	gi|166406891|gb|EU244393.1|	80.85	94	4e-15	89.7	36095	N/A	N/A	N/A	75
Roberts_20100712_CC_F3_trimmed_contig_14	gi|91992331|gb|DQ453716.1|	gi|91992331|gb|DQ453716.1|	97.65	213	1e-96	 361	6454	N/A	N/A	N/A	76
Roberts_20100712_CC_F3_trimmed_contig_15	gi|345492297|ref|XM_001600219.2|	gi|345492297|ref|XM_001600219.2|	75.89	112	2e-12	80.6	7425	N/A	N/A	N/A	100

In [6]:

!blastn -help

USAGE
  blastn [-h] [-help] [-import_search_strategy filename]
    [-export_search_strategy filename] [-task task_name] [-db database_name]
    [-dbsize num_letters] [-gilist filename] [-seqidlist filename]
    [-negative_gilist filename] [-entrez_query entrez_query]
    [-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm]
    [-subject subject_input_file] [-subject_loc range] [-query input_file]
    [-out output_file] [-evalue evalue] [-word_size int_value]
    [-gapopen open_penalty] [-gapextend extend_penalty]
    [-perc_identity float_value] [-xdrop_ungap float_value]
    [-xdrop_gap float_value] [-xdrop_gap_final float_value]
    [-searchsp int_value] [-max_hsps_per_subject int_value] [-penalty penalty]
    [-reward reward] [-no_greedy] [-min_raw_gapped_score int_value]
    [-template_type type] [-template_length int_value] [-dust DUST_options]
    [-filtering_db filtering_database]
    [-window_masker_taxid window_masker_taxid]
    [-window_masker_db window_masker_db] [-soft_masking soft_masking]
    [-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value]
    [-best_hit_score_edge float_value] [-window_size int_value]
    [-off_diagonal_range int_value] [-use_index boolean] [-index_name string]
    [-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines]
    [-outfmt format] [-show_gis] [-num_descriptions int_value]
    [-num_alignments int_value] [-html] [-max_target_seqs num_sequences]
    [-num_threads int_value] [-remote] [-version]

DESCRIPTION
   Nucleotide-Nucleotide BLAST 2.2.28+

OPTIONAL ARGUMENTS
 -h
   Print USAGE and DESCRIPTION;  ignore all other parameters
 -help
   Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
 -version
   Print version number;  ignore other arguments

 *** Input query options
 -query <File_In>
   Input file name
   Default = `-'
 -query_loc <String>
   Location on the query sequence in 1-based offsets (Format: start-stop)
 -strand <String, `both', `minus', `plus'>
   Query strand(s) to search against database/subject
   Default = `both'

 *** General search options
 -task <String, Permissible values: 'blastn' 'blastn-short' 'dc-megablast'
                'megablast' 'rmblastn' >
   Task to execute
   Default = `megablast'
 -db <String>
   BLAST database name
    * Incompatible with:  subject, subject_loc
 -out <File_Out>
   Output file name
   Default = `-'
 -evalue <Real>
   Expectation value (E) threshold for saving hits 
   Default = `10'
 -word_size <Integer, >=4>
   Word size for wordfinder algorithm (length of best perfect match)
 -gapopen <Integer>
   Cost to open a gap
 -gapextend <Integer>
   Cost to extend a gap
 -penalty <Integer, <=0>
   Penalty for a nucleotide mismatch
 -reward <Integer, >=0>
   Reward for a nucleotide match
 -use_index <Boolean>
   Use MegaBLAST database index
 -index_name <String>
   MegaBLAST database index name

 *** BLAST-2-Sequences options
 -subject <File_In>
   Subject sequence(s) to search
    * Incompatible with:  db, gilist, seqidlist, negative_gilist,
   db_soft_mask, db_hard_mask
 -subject_loc <String>
   Location on the subject sequence in 1-based offsets (Format: start-stop)
    * Incompatible with:  db, gilist, seqidlist, negative_gilist,
   db_soft_mask, db_hard_mask, remote

 *** Formatting options
 -outfmt <String>
   alignment view options:
     0 = pairwise,
     1 = query-anchored showing identities,
     2 = query-anchored no identities,
     3 = flat query-anchored, show identities,
     4 = flat query-anchored, no identities,
     5 = XML Blast output,
     6 = tabular,
     7 = tabular with comment lines,
     8 = Text ASN.1,
     9 = Binary ASN.1,
    10 = Comma-separated values,
    11 = BLAST archive format (ASN.1) 
   
   Options 6, 7, and 10 can be additionally configured to produce
   a custom format specified by space delimited format specifiers.
   The supported format specifiers are:
   	    qseqid means Query Seq-id
   	       qgi means Query GI
   	      qacc means Query accesion
   	   qaccver means Query accesion.version
   	      qlen means Query sequence length
   	    sseqid means Subject Seq-id
   	 sallseqid means All subject Seq-id(s), separated by a ';'
   	       sgi means Subject GI
   	    sallgi means All subject GIs
   	      sacc means Subject accession
   	   saccver means Subject accession.version
   	   sallacc means All subject accessions
   	      slen means Subject sequence length
   	    qstart means Start of alignment in query
   	      qend means End of alignment in query
   	    sstart means Start of alignment in subject
   	      send means End of alignment in subject
   	      qseq means Aligned part of query sequence
   	      sseq means Aligned part of subject sequence
   	    evalue means Expect value
   	  bitscore means Bit score
   	     score means Raw score
   	    length means Alignment length
   	    pident means Percentage of identical matches
   	    nident means Number of identical matches
   	  mismatch means Number of mismatches
   	  positive means Number of positive-scoring matches
   	   gapopen means Number of gap openings
   	      gaps means Total number of gaps
   	      ppos means Percentage of positive-scoring matches
   	    frames means Query and subject frames separated by a '/'
   	    qframe means Query frame
   	    sframe means Subject frame
   	      btop means Blast traceback operations (BTOP)
   	   staxids means Subject Taxonomy ID(s), separated by a ';'
   	 sscinames means Subject Scientific Name(s), separated by a ';'
   	 scomnames means Subject Common Name(s), separated by a ';'
   	sblastnames means Subject Blast Name(s), separated by a ';'
   			 (in alphabetical order)
   	sskingdoms means Subject Super Kingdom(s), separated by a ';'
   			 (in alphabetical order) 
   	    stitle means Subject Title
   	salltitles means All Subject Title(s), separated by a '<>'
   	   sstrand means Subject Strand
   	     qcovs means Query Coverage Per Subject
   	   qcovhsp means Query Coverage Per HSP
   When not provided, the default value is:
   'qseqid sseqid pident length mismatch gapopen qstart qend sstart send
   evalue bitscore', which is equivalent to the keyword 'std'
   Default = `0'
 -show_gis
   Show NCBI GIs in deflines?
 -num_descriptions <Integer, >=0>
   Number of database sequences to show one-line descriptions for
   Not applicable for outfmt > 4
   Default = `500'
    * Incompatible with:  max_target_seqs
 -num_alignments <Integer, >=0>
   Number of database sequences to show alignments for
   Default = `250'
    * Incompatible with:  max_target_seqs
 -html
   Produce HTML output?

 *** Query filtering options
 -dust <String>
   Filter query sequence with DUST (Format: 'yes', 'level window linker', or
   'no' to disable)
   Default = `20 64 1'
 -filtering_db <String>
   BLAST database containing filtering elements (i.e.: repeats)
 -window_masker_taxid <Integer>
   Enable WindowMasker filtering using a Taxonomic ID
 -window_masker_db <String>
   Enable WindowMasker filtering using this repeats database.
 -soft_masking <Boolean>
   Apply filtering locations as soft masks
   Default = `true'
 -lcase_masking
   Use lower case filtering in query and subject sequence(s)?

 *** Restrict search or results
 -gilist <String>
   Restrict search of database to list of GI's
    * Incompatible with:  negative_gilist, seqidlist, remote, subject,
   subject_loc
 -seqidlist <String>
   Restrict search of database to list of SeqId's
    * Incompatible with:  gilist, negative_gilist, remote, subject,
   subject_loc
 -negative_gilist <String>
   Restrict search of database to everything except the listed GIs
    * Incompatible with:  gilist, seqidlist, remote, subject, subject_loc
 -entrez_query <String>
   Restrict search with the given Entrez query
    * Requires:  remote
 -db_soft_mask <String>
   Filtering algorithm ID to apply to the BLAST database as soft masking
    * Incompatible with:  db_hard_mask, subject, subject_loc
 -db_hard_mask <String>
   Filtering algorithm ID to apply to the BLAST database as hard masking
    * Incompatible with:  db_soft_mask, subject, subject_loc
 -perc_identity <Real, 0..100>
   Percent identity
 -culling_limit <Integer, >=0>
   If the query range of a hit is enveloped by that of at least this many
   higher-scoring hits, delete the hit
    * Incompatible with:  best_hit_overhang, best_hit_score_edge
 -best_hit_overhang <Real, (>=0 and =<0.5)>
   Best Hit algorithm overhang value (recommended value: 0.1)
    * Incompatible with:  culling_limit
 -best_hit_score_edge <Real, (>=0 and =<0.5)>
   Best Hit algorithm score edge value (recommended value: 0.1)
    * Incompatible with:  culling_limit
 -max_target_seqs <Integer, >=1>
   Maximum number of aligned sequences to keep 
   Not applicable for outfmt <= 4
   Default = `500'
    * Incompatible with:  num_descriptions, num_alignments

 *** Discontiguous MegaBLAST options
 -template_type <String, `coding', `coding_and_optimal', `optimal'>
   Discontiguous MegaBLAST template type
    * Requires:  template_length
 -template_length <Integer, Permissible values: '16' '18' '21' >
   Discontiguous MegaBLAST template length
    * Requires:  template_type

 *** Statistical options
 -dbsize <Int8>
   Effective length of the database 
 -searchsp <Int8, >=0>
   Effective length of the search space
 -max_hsps_per_subject <Integer, >=0>
   Override maximum number of HSPs per subject to save for ungapped searches
   (0 means do not override)
   Default = `0'

 *** Search strategy options
 -import_search_strategy <File_In>
   Search strategy to use
    * Incompatible with:  export_search_strategy
 -export_search_strategy <File_Out>
   File name to record the search strategy used
    * Incompatible with:  import_search_strategy

 *** Extension options
 -xdrop_ungap <Real>
   X-dropoff value (in bits) for ungapped extensions
 -xdrop_gap <Real>
   X-dropoff value (in bits) for preliminary gapped extensions
 -xdrop_gap_final <Real>
   X-dropoff value (in bits) for final gapped alignment
 -no_greedy
   Use non-greedy dynamic programming extension
 -min_raw_gapped_score <Integer>
   Minimum raw gapped score to keep an alignment in the preliminary gapped and
   traceback stages
 -ungapped
   Perform ungapped alignment only?
 -window_size <Integer, >=0>
   Multiple hits window size, use 0 to specify 1-hit algorithm
 -off_diagonal_range <Integer, >=0>
   Number of off-diagonals to search for the 2nd hit, use 0 to turn off
   Default = `0'

 *** Miscellaneous options
 -parse_deflines
   Should the query and subject defline(s) be parsed?
 -num_threads <Integer, >=1>
   Number of threads (CPUs) to use in the BLAST search
   Default = `1'
    * Incompatible with:  remote
 -remote
   Execute search remotely?
    * Incompatible with:  gilist, seqidlist, negative_gilist, subject_loc,
   num_threads

!blastn -query /Volumes/web/cnidarian/BlackAbalone_Contigs_v3.fa -db /Volumes/Bay3/CLC_blastdatabases/nt -out /Volumes/web/cnidarian/lft_BlackAbalone_v3_nt_blastout_taxa2 -outfmt "6 std stitle staxids sscinames scomnames sblastnames" -evalue 1E-10 -max_target_seqs 1 -task blastn

In [25]:

!head /Volumes/web/cnidarian/lft_BlackAbalone_v3_nt_blastout_taxa2

Roberts_20100712_CC_F3_trimmed_contig_2	gi|115947556|ref|XM_796732.2|	84.21	114	18	0	2	115	605	718	7e-26	 125	PREDICTED: Strongylocentrotus purpuratus similar to MGC80921 protein, transcript variant 2 (LOC578948), partial mRNA	7668	N/A	N/A	N/A
Roberts_20100712_CC_F3_trimmed_contig_4	gi|177667010|gb|EU595789.1|	85.97	221	31	0	3	223	9228	9008	8e-66	 259	Haliotis discus hannai mitochondrion, partial genome	42344	N/A	N/A	N/A
Roberts_20100712_CC_F3_trimmed_contig_6	gi|345329379|ref|XM_001506155.2|	86.96	161	21	0	1	161	60	220	5e-47	 196	PREDICTED: Ornithorhynchus anatinus 40S ribosomal protein S3-A-like (LOC100074614), partial mRNA	9258	N/A	N/A	N/A
Roberts_20100712_CC_F3_trimmed_contig_9	gi|306922143|dbj|AB490993.1|	88.67	203	23	0	5	207	364	566	6e-67	 262	Sebastes schlegelii mRNA, clone: BRF 39-G6, induced by treatment of LPS	214486	N/A	N/A	N/A
Roberts_20100712_CC_F3_trimmed_contig_9	gi|306922143|dbj|AB490993.1|	87.25	204	25	1	5	207	592	795	1e-62	 248	Sebastes schlegelii mRNA, clone: BRF 39-G6, induced by treatment of LPS	214486	N/A	N/A	N/A
Roberts_20100712_CC_F3_trimmed_contig_9	gi|306922143|dbj|AB490993.1|	85.71	203	29	0	5	207	136	338	9e-59	 235	Sebastes schlegelii mRNA, clone: BRF 39-G6, induced by treatment of LPS	214486	N/A	N/A	N/A
Roberts_20100712_CC_F3_trimmed_contig_9	gi|306922143|dbj|AB490993.1|	90.00	110	11	0	98	207	1	110	1e-32	 149	Sebastes schlegelii mRNA, clone: BRF 39-G6, induced by treatment of LPS	214486	N/A	N/A	N/A
Roberts_20100712_CC_F3_trimmed_contig_10	gi|166406891|gb|EU244393.1|	80.85	94	18	0	12	105	133	226	4e-15	89.7	Haliotis diversicolor clone HDr4CJ446 CD63 antigen-like protein mRNA, partial cds	36095	N/A	N/A	N/A
Roberts_20100712_CC_F3_trimmed_contig_14	gi|91992331|gb|DQ453716.1|	97.65	213	5	0	1	213	955	1167	1e-96	 361	Haliotis rufescens vitelline envelope zona pellucida domain 3 (VEZP3) mRNA, complete cds	6454	N/A	N/A	N/A
Roberts_20100712_CC_F3_trimmed_contig_15	gi|345492297|ref|XM_001600219.2|	75.89	112	27	0	1	112	225	336	2e-12	80.6	PREDICTED: Nasonia vitripennis 60S ribosomal protein L22-like (LOC100115956), mRNA	7425	N/A	N/A	N/A

GENE DESCRIPTION AND Tax IDs produced

In [7]:

!sed 's/Roberts_20100712_CC_F3_trimmed_/BlackAbalone_v3_/g' </Volumes/web/cnidarian/lft_BlackAbalone_v3_nt_blastout_taxa2> /Volumes/web/cnidarian/lft_BlackAbalone_v3_nt_blastout_taxa3
#sed 's/abc/XYZ/g' <infile> outfile

In [8]:

!head /Volumes/web/cnidarian/lft_BlackAbalone_v3_nt_blastout_taxa3

BlackAbalone_v3_contig_2	gi|115947556|ref|XM_796732.2|	84.21	114	18	0	2	115	605	718	7e-26	 125	PREDICTED: Strongylocentrotus purpuratus similar to MGC80921 protein, transcript variant 2 (LOC578948), partial mRNA	7668	N/A	N/A	N/A
BlackAbalone_v3_contig_4	gi|177667010|gb|EU595789.1|	85.97	221	31	0	3	223	9228	9008	8e-66	 259	Haliotis discus hannai mitochondrion, partial genome	42344	N/A	N/A	N/A
BlackAbalone_v3_contig_6	gi|345329379|ref|XM_001506155.2|	86.96	161	21	0	1	161	60	220	5e-47	 196	PREDICTED: Ornithorhynchus anatinus 40S ribosomal protein S3-A-like (LOC100074614), partial mRNA	9258	N/A	N/A	N/A
BlackAbalone_v3_contig_9	gi|306922143|dbj|AB490993.1|	88.67	203	23	0	5	207	364	566	6e-67	 262	Sebastes schlegelii mRNA, clone: BRF 39-G6, induced by treatment of LPS	214486	N/A	N/A	N/A
BlackAbalone_v3_contig_9	gi|306922143|dbj|AB490993.1|	87.25	204	25	1	5	207	592	795	1e-62	 248	Sebastes schlegelii mRNA, clone: BRF 39-G6, induced by treatment of LPS	214486	N/A	N/A	N/A
BlackAbalone_v3_contig_9	gi|306922143|dbj|AB490993.1|	85.71	203	29	0	5	207	136	338	9e-59	 235	Sebastes schlegelii mRNA, clone: BRF 39-G6, induced by treatment of LPS	214486	N/A	N/A	N/A
BlackAbalone_v3_contig_9	gi|306922143|dbj|AB490993.1|	90.00	110	11	0	98	207	1	110	1e-32	 149	Sebastes schlegelii mRNA, clone: BRF 39-G6, induced by treatment of LPS	214486	N/A	N/A	N/A
BlackAbalone_v3_contig_10	gi|166406891|gb|EU244393.1|	80.85	94	18	0	12	105	133	226	4e-15	89.7	Haliotis diversicolor clone HDr4CJ446 CD63 antigen-like protein mRNA, partial cds	36095	N/A	N/A	N/A
BlackAbalone_v3_contig_14	gi|91992331|gb|DQ453716.1|	97.65	213	5	0	1	213	955	1167	1e-96	 361	Haliotis rufescens vitelline envelope zona pellucida domain 3 (VEZP3) mRNA, complete cds	6454	N/A	N/A	N/A
BlackAbalone_v3_contig_15	gi|345492297|ref|XM_001600219.2|	75.89	112	27	0	1	112	225	336	2e-12	80.6	PREDICTED: Nasonia vitripennis 60S ribosomal protein L22-like (LOC100115956), mRNA	7425	N/A	N/A	N/A

SELECT id, foldchange, pval, de.Column3 as SPID, evalue, Column13 as NCBI_nt_Des FROM [lisa418@washington.edu].[BlkAb_DESeq_SPID]de left join [sr320@washington.edu].[lft_BlackAbalone_v3_nt_blastout_taxa3]lft on de.id = lft.Column1

In [ ]:

SELECT 
 id,
 foldchange,
 pval,
 Column13 as NCBI_nt_Des
  
  FROM [lisa418@washington.edu].[BlackAB_DESeq.txt]de
  left join [sr320@washington.edu].[lft_BlackAbalone_v3_nt_blastout_taxa3]lft
  on
  de.id = lft.Column1​

@fu Try to get taxID from SP blast

Multi-species Blast¶

code ./blastn -query /Volumes/web-1/cnidarian/BlackAbalone_Contigs_v3.fa -db /Volumes/web-1/whale/fish546/blast/db/Haliotis_kam_transcriptome -out /Volumes/web-1/cnidarian/lft_BlackAbalone_v3_Hal_kam_blastout -outfmt 6 -evalue 1E-5 -max_target_seqs 1 -num_threads 2 -task blastn

In [11]:

!head /Volumes/web/cnidarian/lft_BlackAbalone_v3_Hal_kam_blastout

Roberts_20100712_CC_F3_trimmed_contig_2	Haliotis_kam_contig3505	98.50	133	2	0	1	133	70	202	6e-62	 232
Roberts_20100712_CC_F3_trimmed_contig_4	Haliotis_kam_contig17	90.13	223	22	0	1	223	1408	1186	2e-83	 304
Roberts_20100712_CC_F3_trimmed_contig_5	Haliotis_kam_contig4402	92.68	355	9	2	1	338	388	34	4e-151	 529
Roberts_20100712_CC_F3_trimmed_contig_6	Haliotis_kam_contig272	100.00	173	0	0	1	173	38	210	2e-86	 313
Roberts_20100712_CC_F3_trimmed_contig_9	Haliotis_kam_contig1153	98.45	129	2	0	1	129	129	1	1e-59	 224
Roberts_20100712_CC_F3_trimmed_contig_10	Haliotis_kam_contig59	85.42	96	14	0	10	105	1230	1135	1e-25	 111
Roberts_20100712_CC_F3_trimmed_contig_15	Haliotis_kam_contig455	100.00	112	0	0	1	112	300	189	2e-53	 203
Roberts_20100712_CC_F3_trimmed_contig_19	Haliotis_kam_contig3534	85.14	222	33	0	412	633	223	2	4e-67	 251
Roberts_20100712_CC_F3_trimmed_contig_28	Haliotis_kam_contig329	96.36	165	6	0	1	165	337	501	8e-74	 271
Roberts_20100712_CC_F3_trimmed_contig_30	Haliotis_kam_contig854	98.82	85	1	0	1	85	557	641	3e-37	 149

In [12]:

!tail /Volumes/web/cnidarian/lft_BlackAbalone_v3_Hal_kam_blastout

Roberts_20100712_CC_F3_trimmed_contig_13830	Haliotis_kam_contig2270	97.06	136	3	1	1	135	240	105	8e-60	 224
Roberts_20100712_CC_F3_trimmed_contig_13832	Haliotis_kam_contig2911	97.06	102	3	0	9	110	185	84	1e-43	 170
Roberts_20100712_CC_F3_trimmed_contig_13838	Haliotis_kam_contig6166	94.19	86	5	0	6	91	135	220	3e-32	 132
Roberts_20100712_CC_F3_trimmed_contig_13843	Haliotis_kam_contig4288	96.15	130	5	0	45	174	10	139	6e-56	 212
Roberts_20100712_CC_F3_trimmed_contig_13850	Haliotis_kam_contig4288	83.53	85	14	0	2	86	138	222	1e-19	91.5
Roberts_20100712_CC_F3_trimmed_contig_13851	Haliotis_kam_contig413	96.67	60	2	0	1	60	510	569	2e-22	 100
Roberts_20100712_CC_F3_trimmed_contig_13855	Haliotis_kam_contig6826	84.62	130	19	1	2	130	195	66	7e-35	 141
Roberts_20100712_CC_F3_trimmed_contig_13860	Haliotis_kam_contig911	71.90	121	28	2	13	129	121	3	6e-11	62.6
Roberts_20100712_CC_F3_trimmed_contig_13870	Haliotis_kam_contig2899	100.00	51	0	0	1	51	51	1	2e-20	93.3
Roberts_20100712_CC_F3_trimmed_contig_13873	Haliotis_kam_contig1191	97.20	107	3	0	1	107	821	715	2e-46	 179

In [13]:

!grep -c "Roberts" /Volumes/web/cnidarian/lft_BlackAbalone_v3_Hal_kam_blastout

code
./blastn -query /Volumes/web-1/cnidarian/BlackAbalone_Contigs_v3.fa -db /Volumes/web-1/whale/fish546/blast/db/Haliotis_midae_franchini -out /Volumes/web-1/cnidarian/lft_BlackAbalone_v3_Hal_midae_blastout -outfmt 6 -evalue 1E-5 -max_target_seqs 1 -num_threads 2 -task blastn

In [14]:

!head /Volumes/web/cnidarian/lft_BlackAbalone_v3_Hal_midae_blastout

Roberts_20100712_CC_F3_trimmed_contig_1	Contig_3052_Coverage_84.98	90.65	107	10	0	2	108	201	95	6e-37	 149
Roberts_20100712_CC_F3_trimmed_contig_2	Contig_6000_Coverage_67.17	95.33	107	5	0	1	107	109	3	3e-43	 170
Roberts_20100712_CC_F3_trimmed_contig_3	Contig_18668_Coverage_137.10	85.45	55	8	0	34	88	622	568	2e-11	64.4
Roberts_20100712_CC_F3_trimmed_contig_4	Contig_22684_Coverage_350.78	86.36	66	9	0	21	86	553	618	2e-15	78.8
Roberts_20100712_CC_F3_trimmed_contig_5	Contig_5029_Coverage_76.79	81.44	194	32	3	48	240	282	92	4e-45	 178
Roberts_20100712_CC_F3_trimmed_contig_7	Contig_1511_Coverage_54.42	90.30	237	23	0	181	417	297	61	6e-89	 324
Roberts_20100712_CC_F3_trimmed_contig_8	Contig_789_Coverage_53.73	87.00	100	13	0	1	100	634	535	7e-29	 122
Roberts_20100712_CC_F3_trimmed_contig_9	Contig_21030_Coverage_485.53	91.75	206	17	0	2	207	205	410	1e-80	 295
Roberts_20100712_CC_F3_trimmed_contig_10	Contig_290_Coverage_208.28	82.98	94	16	0	12	105	610	703	1e-21	98.7
Roberts_20100712_CC_F3_trimmed_contig_11	Contig_4226_Coverage_62.51	85.00	80	12	0	66	145	477	556	2e-19	91.5

In [15]:

!tail /Volumes/web/cnidarian/lft_BlackAbalone_v3_Hal_midae_blastout

Roberts_20100712_CC_F3_trimmed_contig_13839	Contig_13235_Coverage_19.54	87.39	111	14	0	4	114	41	151	1e-33	 138
Roberts_20100712_CC_F3_trimmed_contig_13847	Contig_94_Coverage_67.50	83.65	104	17	0	1	104	726	623	2e-25	 111
Roberts_20100712_CC_F3_trimmed_contig_13853	Contig_16227_Coverage_53.40	82.14	56	8	1	3	58	56	109	5e-08	53.6
Roberts_20100712_CC_F3_trimmed_contig_13855	Contig_6084_Coverage_35.44	86.67	120	16	0	1	120	350	231	9e-36	 145
Roberts_20100712_CC_F3_trimmed_contig_13857	Contig_94_Coverage_67.50	89.17	157	17	0	1	157	190	34	4e-54	 206
Roberts_20100712_CC_F3_trimmed_contig_13859	Contig_17733_Coverage_12.63	91.18	34	3	0	47	80	18	51	2e-06	48.2
Roberts_20100712_CC_F3_trimmed_contig_13860	Contig_2605_Coverage_135.73	71.32	129	36	1	13	140	917	1045	9e-11	62.6
Roberts_20100712_CC_F3_trimmed_contig_13861	Contig_21412_Coverage_92.26	74.53	106	22	2	16	116	227	122	6e-12	66.2
Roberts_20100712_CC_F3_trimmed_contig_13879	Contig_10459_Coverage_16.77	74.47	94	24	0	8	101	44	137	7e-11	62.6
Roberts_20100712_CC_F3_trimmed_contig_13883	Contig_3412_Coverage_65.56	76.83	82	16	2	1	81	471	550	3e-09	57.2

In [16]:

!grep -c "Roberts" /Volumes/web/cnidarian/lft_BlackAbalone_v3_Hal_midae_blastout

In [ ]:

#running blackAb versus other Abalone at 1e-20

In [46]:

!blastn -query /Volumes/web/cnidarian/BlackAbalone_Contigs_v3.fa -db /Volumes/web/whale/fish546/blast/db/Haliotis_rufescens_transcriptome -out /Volumes/web/cnidarian/lft_BlackAbalone_v3_Hal_ruf_blastout -outfmt 6 -evalue 1E-20 -max_target_seqs 1 -num_threads 2 -task blastn

In [47]:

!blastn -query /Volumes/web/cnidarian/BlackAbalone_Contigs_v3.fa -db /Volumes/web/whale/fish546/blast/db/Haliotis_midae_franchini -out /Volumes/web/cnidarian/lft_BlackAbalone_v3_Hal_midae_blastout_b -outfmt 6 -evalue 1E-20 -max_target_seqs 1 -num_threads 2 -task blastn

In [48]:

!blastn -query /Volumes/web/cnidarian/BlackAbalone_Contigs_v3.fa -db /Volumes/web/whale/fish546/blast/db/Haliotis_kam_transcriptome -out /Volumes/web/cnidarian/lft_BlackAbalone_v3_Hal_kam_blastout_b -outfmt 6 -evalue 1E-20 -max_target_seqs 1 -num_threads 2 -task blastn

Comparing to OrthoDB - Lottia gigantea¶

Modified from Emma's paper..
To quantify the completeness of the transcriptome, contigs were assessed to determine if they contained orthologs to proteins found in all Metazoa. Specifically, OrthoDB (Waterhouse et al. 2011, http://cegg.unige.ch/orthodb6) was used to obtain a suite of proteins from Lottia gigantea (the giant owl limpet) found as single copy, which have orthologs in all other metazoans in OrthoDB. Sequence comparisons (tBLASTn; Altschul et al. 1997) were performed to find matching contigs. An e-value threshold of 1.0E-10 was used.

Details at https://www.evernote.com/shard/s10/sh/8aa69a54-13fd-4bea-8a09-7f6a08c30fe5/63597cc40252a36bc030000d88cf0f1d

In [1]:

!head /Volumes/web/cnidarian/OrthDB_meta_Lotgi1.fa

>AAEL010815 AAEL010815-PA Q0IED2 Putative uncharacterized protein IPR001060,IPR018808 EOG62FZF8 AAEGY
GEKNNGYEVLYQNMKYGLSATKELAEYFRERSNLEEYNSKLLTKLANKAGSGGGGTFSPLWIILKSTTERLSELHAAKVQ
KLTELVKNINKYAEELHKKHKSVKEEESSTQDAVHAMKESTTAVAKAKDVYNTRLQELEKARKDNSAKEIEKSEAKLRKQ
QDDYKALVEKHNIIKQEFEKKMTITCKRFQEIEEAHLKQMKEFLTSYMEIVQNNFDLVGQVHSDLKRQFLELTVDKLLEQ
FVLNKYTGLEKPEFIELDLVKLGSRSLGTTATAATSNNQLLINTSMPNATSGGSVTTVAEGSVTDSPALSSAAVPTNSPV
NLSTSPPASGGRGSLLDALGGSTDRPMSPAAAGDSSASSSAQSTAKTRSRESRDSTTSGGADSVSTSTAGGAGGGGGGSA
ISAPTSPNDVHNSNQHGGSNNSNGLASTFIGRNALLRGSKCKCSIDFFSPNSVYLSIWSRREKAKSKKTKKKKDSTENCK
TFRCVSICNRTSHNRCIEVYSNFYKTVALKFSILIVFSFENITSFESSSFISEDKDETTKASDAASSNLQTTSAVSTGNV
APTATPEVDEDGYSIQPRETTWDSTTLTEKSNNFYSSSDSDSEDERGERKIHVEIKPLNNGAAPISASVDELRATVENLS
LSPIGALSSRSQSVSQQLGDRPSNGNDPPNASNASTPTTVHPYAPLQSPTLSMSTTSNNRYADLGDIFSEVGDISASAPA

In [4]:

!fgrep -c ">" /Volumes/web/cnidarian/OrthDB_meta_Lotgi1.fa

In [6]:

!makeblastdb -in /Volumes/web/cnidarian/BlackAbalone_Contigs_v3.fa -dbtype nucl -out /Volumes/Bay3/Software/ncbi-blast-2.2.27\+/db/BlackAbalone_Contigs_v3


Building a new DB, current time: 07/17/2013 08:36:07
New DB name:   /Volumes/Bay3/Software/ncbi-blast-2.2.27+/db/BlackAbalone_Contigs_v3
New DB title:  /Volumes/web/cnidarian/BlackAbalone_Contigs_v3.fa
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 13884 sequences in 0.828346 seconds.

In [7]:

!tblastn -query /Volumes/Bay3/Software/ncbi-blast-2.2.26+/query/OrthDB_meta_Lotgi1.fa -db /Volumes/Bay3/Software/ncbi-blast-2.2.27\+/db/BlackAbalone_Contigs_v3 -outfmt 6 -out /Volumes/web/cnidarian/OrthoDB_Lotgi1_BlackAb_v3_tblastn.txt -max_target_seqs 1 -num_threads 2 -evalue 1E-10

In [29]:

!tblastn -query /Volumes/Bay3/Software/ncbi-blast-2.2.26+/query/OrthDB_meta_Lotgi1.fa -db /Volumes/Bay3/Software/ncbi-blast-2.2.27\+/db/BlackAbalone_Contigs_v3 -outfmt 6 -out /Volumes/web/cnidarian/OrthoDB_Lotgi1_BlackAb_v3_tblastn_b.txt -max_target_seqs 1 -num_threads 3 -evalue 1E-20

In [30]:

!head /Volumes/web/cnidarian/OrthoDB_Lotgi1_BlackAb_v3_tblastn_b.txt

AAEL010318	Roberts_20100712_CC_F3_trimmed_contig_3682	90.00	60	5	1	73	132	1	177	5e-32	 116
ENSACAG00000011841	Roberts_20100712_CC_F3_trimmed_contig_3682	88.14	59	7	0	82	140	1	177	6e-33	 119
ENSACAG00000002544	Roberts_20100712_CC_F3_trimmed_contig_3682	94.92	59	3	0	50	108	1	177	1e-34	 123
ENSACAG00000016470	Roberts_20100712_CC_F3_trimmed_contig_3682	91.53	59	5	0	82	140	1	177	1e-34	 123
ACEP20785	Roberts_20100712_CC_F3_trimmed_contig_3682	88.33	60	6	1	53	112	1	177	1e-31	 114
ACEP20789	Roberts_20100712_CC_F3_trimmed_contig_3682	90.00	60	5	1	82	141	1	177	2e-32	 117
ADAR004412	Roberts_20100712_CC_F3_trimmed_contig_3682	90.00	60	5	1	82	141	1	177	8e-32	 115
AECH10224	Roberts_20100712_CC_F3_trimmed_contig_3682	88.33	60	6	1	104	163	1	177	2e-31	 115
AECH10223	Roberts_20100712_CC_F3_trimmed_contig_3682	90.00	60	5	1	125	184	1	177	2e-32	 117
g8984	Roberts_20100712_CC_F3_trimmed_contig_3682	90.00	60	5	1	82	141	1	177	1e-32	 117

In [9]:

#wc       Print byte, word, and line counts
!wc /Volumes/web/cnidarian/OrthoDB_Lotgi1_BlackAb_v3_tblastn.txt

     880   10560   87475 /Volumes/web/cnidarian/OrthoDB_Lotgi1_BlackAb_v3_tblastn.txt

In [11]:

!fgrep -c "Roberts_20100712_CC" /Volumes/web/cnidarian/OrthoDB_Lotgi1_BlackAb_v3_tblastn.txt

In [31]:

!fgrep -c "Roberts_20100712_CC" /Volumes/web/cnidarian/OrthoDB_Lotgi1_BlackAb_v3_tblastn_b.txt

In [32]:

!wc /Volumes/web/cnidarian/OrthoDB_Lotgi1_BlackAb_v3_tblastn_b.txt

     828    9936   82229 /Volumes/web/cnidarian/OrthoDB_Lotgi1_BlackAb_v3_tblastn_b.txt

concerned about the fact there are so few black abalone contigs represented here.

http://eagle.fish.washington.edu/cnidarian/OrthoDB_Lotgi1_BlackAb_v3_tblastn.txt

In [15]:

#-A is the number of lines After
!fgrep -A 10 "Roberts_20100712_CC_F3_trimmed_contig_3682" /Volumes/web/cnidarian/BlackAbalone_Contigs_v3.fa

>Roberts_20100712_CC_F3_trimmed_contig_3682 Average coverage: 80.91
ATCAGAATAATGTGGTCTCAACGAGACCCTTCCTTGAGAAAGTCTGGAGTGGGCAATGTG
TTCATCAAGAATTTGGACAAGAGCATCGACAACAAAGCTCTGTATGACACATTCTCTGCT
TTTGGCAACATCCTGTCTTGTAAGATAGCTTCTGATGAAAATGGCTCCAAGGGTTATGG
>Roberts_20100712_CC_F3_trimmed_contig_3683 Average coverage: 18.90
TTGCAATCTAGAAATACGTCCGCTCTTGTACTGTAGCAGTTTTTACAATTACGCCATTGC
ATCGAACCCATTAAGACCAGATCATTTACTCCTAGACGAG
>Roberts_20100712_CC_F3_trimmed_contig_3684 Average coverage: 97.66
GTCTCCTGCCTCTGGTTGGAATTAACAGAAGTGATGAGTTTGTGAAGGAAGTGTGTGATC
AGTGCAGCTTCGCCTCCATGCAGAAAAGCAAGTCACCCATGTCCAAGGTCATGTATAGAA
AAGGTGAGGTT

In [16]:

#in the meantime will blast other Haliotis databases

In [36]:

!tblastn -query /Volumes/Bay3/Software/ncbi-blast-2.2.26+/query/OrthDB_meta_Lotgi1.fa -db /Volumes/web/whale/fish546/blast/db/Haliotis_kam_transcriptome -outfmt 6 -out /Volumes/web/cnidarian/OrthoDB_Lotgi1_Haliotis_kam_tblastn.txt -max_target_seqs 1 -num_threads 1 -evalue 1E-20

In [37]:

!tblastn -query /Volumes/Bay3/Software/ncbi-blast-2.2.26+/query/OrthDB_meta_Lotgi1.fa -db /Volumes/web/whale/fish546/blast/db/Haliotis_midae_franchini -outfmt 6 -out /Volumes/web/cnidarian/OrthoDB_Lotgi1_Haliotis_midae_franchini_tblastn.txt -max_target_seqs 1 -num_threads 1 -evalue 1E-20

In [21]:

!makeblastdb -in /Volumes/web/cnidarian/H.rufescens_contig.fa -dbtype nucl -out /Volumes/web/whale/fish546/blast/db/Haliotis_rufescens_transcriptome


Building a new DB, current time: 07/18/2013 15:46:33
New DB name:   /Volumes/web/whale/fish546/blast/db/Haliotis_rufescens_transcriptome
New DB title:  /Volumes/web/cnidarian/H.rufescens_contig.fa
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 162928 sequences in 19.2224 seconds.

In [38]:

!tblastn -query /Volumes/Bay3/Software/ncbi-blast-2.2.26+/query/OrthDB_meta_Lotgi1.fa -db /Volumes/web/whale/fish546/blast/db/Haliotis_rufescens_transcriptome -outfmt 6 -out /Volumes/web/cnidarian/OrthoDB_Lotgi1_Haliotis_rufescens_tblastn.txt -max_target_seqs 1 -num_threads 1 -evalue 1E-20

In [39]:

!head /Volumes/web/cnidarian/OrthoDB_Lotgi1_Haliotis_kam_tblastn.txt

AAEL010318	Haliotis_kam_contig350	76.46	429	93	5	1	423	235	1515	0.0	 679
ENSACAG00000011841	Haliotis_kam_contig350	60.55	659	229	11	1	651	208	2115	0.0	 723
ENSACAG00000002544	Haliotis_kam_contig350	65.60	593	189	6	4	585	313	2079	0.0	 740
ENSACAG00000016470	Haliotis_kam_contig350	66.67	627	193	8	1	614	208	2079	0.0	 800
ACEP20785	Haliotis_kam_contig350	66.04	583	165	12	36	595	400	2118	0.0	 690
ACEP20789	Haliotis_kam_contig350	69.40	647	175	10	1	634	208	2118	0.0	 843
ADAR004412	Haliotis_kam_contig350	62.10	657	205	11	1	640	208	2097	0.0	 734
AECH10224	Haliotis_kam_contig350	67.41	669	173	12	1	656	208	2118	0.0	 826
AECH10223	Haliotis_kam_contig350	65.36	690	173	12	1	677	208	2118	0.0	 826
g8984	Haliotis_kam_contig350	70.59	646	164	10	1	629	208	2118	0.0	 891

In [40]:

!wc /Volumes/web/cnidarian/OrthoDB_Lotgi1_Haliotis_kam_tblastn.txt

     438    5256   35941 /Volumes/web/cnidarian/OrthoDB_Lotgi1_Haliotis_kam_tblastn.txt

In [41]:

!head /Volumes/web/cnidarian/OrthoDB_Lotgi1_Haliotis_midae_franchini_tblastn.txt

gi|221125234|ref|XP_002165797.1|	Contig_3019_Coverage_17.03	55.00	80	36	0	1	80	274	35	5e-25	97.4
g8694	Contig_1661_Coverage_123.10	37.29	177	97	2	1714	1877	679	152	1e-34	 135
AAEL000339	Contig_308_Coverage_33.26	38.55	166	98	2	255	416	1	498	1e-35	 131
ENSACAG00000006114	Contig_308_Coverage_33.26	37.95	166	99	2	361	522	1	498	5e-34	 127
ENSACAG00000006855	Contig_308_Coverage_33.26	39.16	166	97	2	145	306	1	498	2e-37	 135
ENSACAG00000003680	Contig_308_Coverage_33.26	37.35	166	100	2	326	487	1	498	5e-32	 121
ACEP15907	Contig_308_Coverage_33.26	38.79	165	97	2	230	390	1	495	4e-36	 132
ADAR002823	Contig_308_Coverage_33.26	39.88	163	94	2	118	276	1	489	5e-37	 131
AECH18169	Contig_308_Coverage_33.26	38.79	165	96	3	347	506	1	495	9e-34	 127
g1442	Contig_308_Coverage_33.26	37.95	166	99	2	319	480	1	498	9e-36	 132

In [42]:

!wc /Volumes/web/cnidarian/OrthoDB_Lotgi1_Haliotis_midae_franchini_tblastn.txt

    1432   17184  122489 /Volumes/web/cnidarian/OrthoDB_Lotgi1_Haliotis_midae_franchini_tblastn.txt

In [43]:

!head /Volumes/web/cnidarian/OrthoDB_Lotgi1_Haliotis_rufescens_tblastn.txt

AAEL010815	contig145	46.44	267	138	3	1	262	90	890	1e-61	 216
ENSACAG00000009572	contig145	46.13	271	142	2	4	274	72	872	1e-76	 255
ENSACAG00000017803	contig145	46.59	264	141	0	1	264	63	854	1e-73	 232
ACEP19080	contig145	48.79	248	126	1	1	247	129	872	4e-74	 249
ADAR004115	contig145	48.25	228	116	2	5	230	72	755	8e-65	 224
AECH14598	contig145	51.31	267	129	1	5	270	72	872	5e-88	 289
g3073	contig145	46.40	250	133	1	1	250	129	875	6e-72	 244
AGAP012683	contig145	46.67	255	134	2	10	262	90	854	6e-66	 212
AGAP002024	contig145	46.30	270	140	3	5	269	72	881	9e-66	 229
ENSAMEG00000010758	contig145	46.27	268	144	0	1	268	63	866	9e-73	 245

In [44]:

!wc /Volumes/web/cnidarian/OrthoDB_Lotgi1_Haliotis_rufescens_tblastn.txt

    5311   63732  377427 /Volumes/web/cnidarian/OrthoDB_Lotgi1_Haliotis_rufescens_tblastn.txt

In [ ]: