How To Blast+ Against A Local Database

Question

[ropni]

hi all,

I need to pull out a specific protein from a transcriptome data deposited in a local server (using linux platform). I have the protein sequence in fasta. I get to know from few papers that i need to use local blast and scan against all protein set.

Can anyone tell me how to use unix bash scripting to pull out the protein from the transcriptomic data by providing a sample scripts how to perform the task? If my Idea is wrong please advice me on a preferable steps. Your favor is much appreciated. thank you

Answer 1

[Benn]

What you probably wanna do is first translate your transcriptome data into proteins data and put it in one big fasta file. This fasta file will be used to make a local db on your computer.

Then, use blast with your specific protein fasta file against this db.

There is a nice manual about how to use blast on unix/linux.

http://www.ncbi.nlm.nih.gov/books/NBK52640/

[ropni]

thank you. I'll try to do this but how to translate my transcriptome data into proteins data? sorry if I'm being very nob but I have to learn from scratch. It would be very helpful to guide me on how to translate them into protein data. Thanks in advance