Protein Sequence charecterization using pBLAST

Question

[Optimist]

Hello Dear Biostars Community,

I've got a set of 11,985 protein sequences (maximum length is 2152 aa and minimum is 59 aa).

Now, the problem is how do I characterize these 11,985 protein sequences with respect to the name of the protein, it's role and origin.

Are there any options like NCBI BLAST, parameters to be used for effective results. Tools and software that can be employed. Literature help is also fine.

Please enlighten me about the way ahead to achieve this.

Thanking you all

yours

Optimist

Answer 1

[h.mon]

InterProScan is probably the best resource for protein annotation. You can try dammit or Trinotate, two good pipelines for transcriptome annotation - they should work with protein only data.

You could also explore this OmicTools list.