Search a proteome file to blast database (command line usage)

Question

[Mehmet]

Dear All:

I have a proteome file generated from Next Gen. Sequencing. I want to search my proteome file against to blast database using command line version. How to do that? Please do not send me manual of blast command line. I know little about Linux. I need a clear explanation of command line usage.

Thank you.

[Michael]

I need a clear explanation of command line usage.

That is difficult without a clear explanation of what kind data you have and what you want to do, lacking issues:

1. NGS doesn't yield proteomes, therefore you might have a transcriptome assembly, which you maybe translated
2. what's the nature of the blast database? nucleotide or protein?
3. what is your desired output format?
4. a clear explanation of command line usage with many examples is contained in the online manual. What have you tried?

[Mehmet]

Hi: I have used trinity for de novo transcriptome assembly, I have generated it. Later, I have used Transdecoder to translate transcripts into amino acids. Now I have proteome file of the transcripts. My point is that I want to see my proteome file ( each protein sequence) matches to which protein in NCBI database.

[natasha.sernova]

If you have a proteome, you can use makeblastdb to make a database out of your translated proteins and search NCBI with each of the proteins from your database with blastp or blastx (whatever you prefer).