How to get gene from PSIBLAST resuts

Question

[tt]

Hello,

I am currently utilizing the local version of PSIBLAST to search for homologous genes by comparing a protein sequence against a protein database. However, I am interested in obtaining the nucleotide sequence from the PSIBLAST results. Although I have access to the genomic sequences of the strains in the database, I am uncertain as to how to retrieve these genes.

Answer 1

[lieven.sterck]

what you likely will need to do:

1. get the ID of the protein that you are interested in (out of result from PSIBLAST)
2. lookup that ID in the gene annotation file of the strain (it is crucial that you have access to the gene annotation files! those are typically in GFF and/or alike formats)
3. get from the annotation file the coordinate set of the gene you want using the ID from above
4. extract (& potentially join) the genomic regions given by the gene annotation file

(without going into too much detail)

UPDATE: coming to think of it, in many situations it's probably enough to take the protein from the PSIBLAST and use it as query for a blastX search against the genome. Much more straightforward and when no annotation file available your only option.

[tt]

Hello, thank you for your answer,

I have a question, Why the information from the GFF file and from the feature table is different? I see CDS in the GFF that are not present in the feature feature table.

Thank you in advance,

[lieven.sterck]

which GFF or feature table?

(do you mean from the GFF and EMBL/genbank file ?)