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azureycy / dbAPIS

dbAPIS is a database of anti-prokaryotic immune system proteins. The repository contains the codes and scripts used to generate and maintain the database.
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A question about hmmsan #2

Open ggl2151 opened 9 months ago

ggl2151 commented 9 months ago

Hello, sorry to bother you again. When I used hmmscan to predict genes in my strain genome (all contigs were translated into amino acid sequences, see genome file contents in Attachment 1) Attachment1 , I found that hmmscan only made predictions on my chromosomal contig sequences, and did not make predictions on some plasmid contigs that followed (as shown in Attachment 2) Attachment2 . However, when I deleted the first chromosomal sequence from the genome file, hmmscan would then predict genes for all the plasmid contigs (as shown in Attachment 3) Attachment3 . I would like to ask if hmmscan supports prediction for WGS data, or if hmmscan can only predict genes for a single amino acid sequence. Thank you.

azureycy commented 8 months ago

Hi @ggl2151 ,

hmmscan can be used to analyze either a single amino acid sequence or multiple sequences. It seems in your Attachment 2 there is a core dumped issue leading to process aborted. There are many "*" in your translated aa sequences, it's recommended to identify the protein-coding regions in the genomic DNA first then translate these regions into aa sequences.