0
$\begingroup$

I'm trying to retrieve the sequence from the gene id in NCBI's nr. If I try doing

blastdbcmd -db nr -entry 1008808716

I get with this result:

>C4TP09.1 RecName: Full=4-hydroxybenzoate 3-monooxygenase (NAD(P)H); AltName: Full=4-hydroxybenzoate 3-hydroxylase; Short=4HB 3-hydroxylase >BAH79107.1 4-hydroxybenzoate 3-hydroxylase [Paenibacillus sp. JJ-1b]
MRTQVGIIGAGPAGLLLSHLLYLQGIESIIIENRTREEIEGTIRAGVLEQGTVDLMNQMGVGARMMKEGHFHEGFELRFN
GRGHRINVHELTGGKYVTVYAQHEVIKDLVAARLQTGGQIHFNVGDVSLHDVDTSSPKIRFRPNKDGELQEIECDFIAGC
DGFRGPSRPAIPQSVRKEYQKVYPFSWLGILVEAPPSAHELIYANHERGFALVSTRSPQIQRLYLQVDAQDHIDNWSDDR
IWSELHARLETRDGFKLLEGPIFQKGIVSMRSFVCDPMQHGRLFLAGDAAHIVPPTGAKGLNLAAADVQVLARGLEAYYK
AGKMEILNRCTEICLRRIWKAERFSWFMTTMLHRDQGHTPFERGIQLAELDYVTSSRAASTSLAENYIGLPMEF

My problem is in the sequence data, which come not only from the gene ID I specified, but also from another identical protein. This is more evident if I do

blastdbcmd -db nr -entry 1008808716 -outfmt "%g"

which outputs only the gene ID. I'd expect it to output the same gene ID I input, but instead this is the output:

1008808716
239937278

I'd like to retrieve sequence data exclusively from the gene ID I input. Is that possible? I tried using different flags in -outfmt, but apparently -outfmt %f overrides any other flag I feed the command.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Browse other questions tagged or ask your own question.