POSSUM Bioinformatics Tool

Question

[Muny]

I am trying to use the POSSUM Bioinformatics tool locally as I want to generate PSSM features using the UniRef100 database as my reference db. POSSUM documentation says that I will need to specify the location of my reference db pssm files aka where I have my UniRef100 pssm files but I can't figure out how to generate or find UniRef100 pssm files online anywhere.

I have the POSSUM stand alone toolkit set up and working, and have successfully tested with the example files. Ideally I would like to generate pssm descriptors by running my aligned sequences against the UniRef100 database. Can anyone help point me in the right directions as to how one would generate a pssm of a reference database like UniRef100 or where I can find it to download? The links I have found searching similar posts here that mention downloads or API's are broken.

Answer 1

[Mensur Dlakic]

The link to all UniRef databases:

https://ftp.uniprot.org/pub/databases/uniprot/uniref/

When you select uniref100, the file you want ends in .fasta.gz and can be downloaded using wget:

wget https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref100/uniref100.fasta.gz

After unpacking with gunzip, you will get a raw database. I don't know exactly how POSSUM works, but it is a safe assumption that you will need to run makeblastdb on the protein file to create indices for BLAST search.

[Muny]

Okay I will give it a try, thank you so much for your response!