cd Volumes/Bay3/Software/ncbi-blast-2.2.29+/db
/Volumes/Bay3/Software/ncbi-blast-2.2.29+/db
!wget http://eagle.fish.washington.edu/cnidarian/Olurida_transcriptome_v3.fasta
--2014-01-10 10:35:25-- http://eagle.fish.washington.edu/cnidarian/Olurida_transcriptome_v3.fasta Resolving eagle.fish.washington.edu... 128.95.149.81 Connecting to eagle.fish.washington.edu|128.95.149.81|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 203983992 (195M) [text/plain] Saving to: `Olurida_transcriptome_v3.fasta' 100%[======================================>] 203,983,992 62.4M/s in 3.1s 2014-01-10 10:35:29 (62.4 MB/s) - `Olurida_transcriptome_v3.fasta' saved [203983992/203983992]
ls
Olurida_transcriptome_v3.fasta uniprot_sprot_r2013_12.pin uniprot_sprot.fasta uniprot_sprot_r2013_12.psq uniprot_sprot_r2013_12.phr
cd bin
/Volumes/Bay3/Software/ncbi-blast-2.2.29+/bin
ls
blast_formatter* deltablast* rpstblastn* blastdb_aliastool* dustmasker* segmasker* blastdbcheck* legacy_blast.pl* tblastn* blastdbcmd* makeblastdb* tblastx* blastn* makembindex* update_blastdb.pl* blastp* makeprofiledb* windowmasker* blastx* psiblast* convert2blastmask* rpsblast*
!makeblastdb -in -dbtype prot -out uniprot_sprot_r2013_12
USAGE makeblastdb [-h] [-help] [-in input_file] [-input_type type] -dbtype molecule_type [-title database_title] [-parse_seqids] [-hash_index] [-mask_data mask_data_files] [-gi_mask] [-gi_mask_name gi_based_mask_names] [-out database_name] [-max_file_sz number_of_bytes] [-taxid TaxID] [-taxid_map TaxIDMapFile] [-logfile File_Name] [-version] DESCRIPTION Application to create BLAST databases, version 2.2.28+ Use '-help' to print detailed descriptions of command line arguments ======================================================================== Error: Argument "dbtype". Mandatory value is missing: `String, `nucl', `prot''
cd db
/Volumes/Bay3/Software/ncbi-blast-2.2.29+/db
!makeblastdb -in Olurida_transcriptome_v3.fasta -dbtype nucl -out Olurida_transcriptome_v3
Building a new DB, current time: 01/10/2014 10:40:05 New DB name: Olurida_transcriptome_v3 New DB title: Olurida_transcriptome_v3.fasta Sequence type: Nucleotide Keep Linkouts: T Keep MBits: T Maximum file size: 1000000000B Adding sequences from FASTA; added 110067 sequences in 9.61759 seconds.
ls
Olurida_transcriptome_v3.fasta uniprot_sprot.fasta Olurida_transcriptome_v3.nhr uniprot_sprot_r2013_12.phr Olurida_transcriptome_v3.nin uniprot_sprot_r2013_12.pin Olurida_transcriptome_v3.nsq uniprot_sprot_r2013_12.psq
pwd
u'/Volumes/Bay3/Software/ncbi-blast-2.2.29+/db'
!head Olurida_transcriptome_v3.fasta
>comp13_c0_seq1 len=486 path=[5581:0-485] ATAAAGAGGATATGATGAATCGACATGATTGGTTAGAAAGGGCAGTATCCAACAGCAATC ACTACATCTTCATTGTGACCAAACAAATGGGAGAAATATTTAATGAACCACTCTCGGAGG AAAGAGAAGATAGAATGCGTTTGTTGACAGAGTGCGAGGATGGAACGTGTGCGTATACAG TCAATTTGATAAGAAACAAATTTATCAAAAGCCGAAAGAACCCTGGATCATGTCACTTGG TAAGTTTTGAAGAGGAGGACGAGAAAGTCGTCTCGCAGTTAAAACATGGACTTCAGTTGT TTCAGAATGTCAGAACACATTGCTACCATTTATATACTGGAAAACGGTTCAGATATAACG CCGCATGCAGCATAATCAATAATATCAAGAAAATAGAGTGATCAAGGAACCGGAAGACTA ATCAGACTTTTGACTGGGTTTCTCAAAAACCTTGGTTCAGCTCAACCAGTGGTTAAATAC TGTGTA