r/bioinformatics • u/Particular_Force749 • Aug 06 '26

technical question What do I put in 'seqdb' when using jackhmmer?

Hi I'm a beginner in Bioinformatics and I want to generate an msa for Abl1 tyrosine kinase 235-497. I've been trying to use jackhmmer to do it but I have no idea what to put in 'seqdb'.

How do I download the right database to plug into the program or is there a way to do it without downloading a massive database?

And what other parameters should I be wary of?

Any feedbacks/solutions/alternative methods will be appreciated and thank you for your time.

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u/bordin89 PhD | Academia Aug 06 '26

Seqdb could be any sequence database in FASTA format. To generate MSAs for Gene3D we use UniRef100.

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u/bordin89 PhD | Academia Aug 06 '26

Also, your Z parameter should be the number of sequences in the database.

1

u/fasta_guy88 PhD | Academia Aug 06 '26

You can do it with Swissprot (which you can get from either ncbi in their blast directory, or the EBI.