Shruti Paniwala
A Bioinformatician
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Blast script to index and extract sequence !!
By Shruti Paniwala 3053 days ago
# look at the file
$ head EC4115.fa
>NC_011353.1 Escherichia coli O157:H7 str. EC4115 chromosome, complete genome.
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTCTC
TGACAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG
TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC
# generate the blast database
$ makeblastdb -dbtype nucl -out EC -in EC4115.fa -parse_seqids
# retreive an entry by id
$ blastdbcmd -db EC -entry 'NC_011353.1' | head
>lcl|NC_011353.1 Escherichia coli O157:H7 str. EC4115 chromosome, complete genome
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTCTCTGACAGCAGCTTCTGAACTG
GTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGAC
....
# query the blast database by id and coordinates
$ blastdbcmd -db EC -range 100-105 -entry 'NC_011353.1'
>lcl|NC_011353.1:100-105 Escherichia coli O157:H7 str. EC4115 chromosome, complete genome
TTAAAA
