Parsing Description from NCBI Blast+

I used BLAST plus to Blast an assembly against a uniprot database, and want to parse the description of the uniprot ID from the uniprot database I am comparing the fasta file to.

blast plus fasta

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updated 10.6 years ago by dschika

• written 10.6 years ago by onspotproductions

How is your blast output file? Is it tabular (-outfmt 6)? What is the uniprot id-description map file like? Post a few example lines please..

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written 10.6 years ago by 5heikki

blastx -db UniprotConus -query /Users/***/Desktop/Cone_Snail_Assembly.txt -outfmt "10 qseqid sallseqid sscinames scomnames sblastnames pident length mismatch gapopen qstart qend sstart send evalue bitscore sseq qseq" -out UniprotConusBLASTFull2.txt

The uniprot is simply a fasta file made into a database using makeblastdb. lines like this e.g.

>sp|P86500|CX21A_CONPU Conotoxin p21a OS=Conus purpurascens PE=1 SV=1
FELLPSQDRSCCIQKTLECLENYPGQASQRAHYCQQDATTNCPDTYYFGCCPGYATCMSI
NAGNNVRSAFDKCINRLCFDPGH

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updated 6.6 years ago by Ram

• written 10.6 years ago by onspotproductions

1 answer

Use grep or e.g. python dictionaries. You may also specify your question...

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written 10.6 years ago by dschika

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