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Protein blast one sequence against custom database

I need to find the best alignment for an amino acidic sequence A in a set of 12467 different sequences located in a multifasta file (including amino acid sequences).

I decided to use blastp generating a database from my file in two different ways (using blast and blastall):

makeblastdb -in db.fasta -dbtype 'prot' -title mydb -out ./mydb
blastp -query seqA.fa -db mydb

And:

blastall -p blastp -d db.fasta -i seqA.fa

Running this my output only includes hits for the general database (all the identifiers for the match are for human genes not included in db.fasta).

How can I run the comparison only against the sequences in my database?

I am also open to other options to do this task.

blast alignment
• 47 views • link
written by samuelmiver samuelmiver

so essentially you are doing the same thing twice.... plus if your database is called mydb why are you putting db.fasta in the second case ??

ps moreover i do not recall if legacy blast can work with formatter from ++. i guess it should but it is always good idea not to mix versions and corresponding tools

• 1 views • link
written by baxy baxy

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