How To Convert Refseq Potein To Corresponding Fasta File Automatically?

Question

[April]

Hi,

I am a beginner of bioinformatic, and I am working on a project which needs to convert the Reseq Protein ID to its FASTA file. Since I have a list of genes, it is really a pain to find each of them on NCBI protein manually. Thus I wonder is there a way find the FASTA file automatically, maybe through some help of web server? Thanks very much.

Answer 1

[Chris]

This thread may give you some insights how to do it in Python.

[April]

Thanks very much. I did look at that before I asked the question, however I have no idea about Python. Anyway, I find this http://www.ncbi.nlm.nih.gov/sites/batchentrez and it really helps me without Python.

Answer 2

[Niek De Klein]

Depending on how many Refseq Protein Id's you have you can put a list of them in the NCBI protein search box. Seperate them by a comma (like this: F56A4.1, F55G11.9). You can then just download the fasta files. If there is a huge amount and you want to use the sequences I would advice reading this urllib2 tutorial to automatically retrieve information from the internet.

[April]

Thank you very much. It seems necessary for me to learn Python. And for this case, I find I can solve it through this: http://www.ncbi.nlm.nih.gov/sites/batchentrez