I would like to generate a protein sequence database for a local installation of BLAST+ and local use of blastp. To make that database, I'll need sequence data.
What are the best sources of human protein sequences to use for this task? I am prioritizing immunological proteins, so I imagine sets that include isoforms or alternative splices are important.
Are there public sources of sequence data available that are focused in this research domain?
Are there are other criteria I should prioritize for immune-related work, which would guide me to build a database using one or another set of sequence data over more generic or general datasets?
Human proteome from UniProt is likely going to be the best curated/latest source of human proteins: https://www.uniprot.org/uniprotkb?query=proteome:UP000005640
If you only want immune related proteins you could use this subset: https://www.uniprot.org/uniprotkb?query=proteome%3AUP000005640+AND+immune
for immune-related work
What are you planning to use this database for?
I am planning to use it for searching for immune-related protein sequences, filtered by similarity and other criteria.
for searching for immune-related protein sequences, filtered by similarity and other criteria.
From patient samples? Since you said blastp, the query would be protein sequence?
Another source of Immune related gene lists: https://www.immport.org/shared/genelists
Yes, the query would be protein sequence. Are there repositories of patient sample data or other domain-specific datasets I would consider?
Log in to answer this question.
