How to retrieve gene symbols with refseq protein accesion number or gi number?

Question

[grayapply2009]

I have about 70,000 refseq protein accession numbers and gi numbers. I want to retrieve gene symbols with these numbers. Obviously the web tool is not enough for this many genes. I am thinking about downloading the ref information for mapping. Here is my previous post: How to get protein names, gene symbols, refseq numbers, gi numbers... using UCSC mysql? The code in my previous code only provides refseq mRNA number while I only have refseq protein number and gi number.

I considered using biomart package in R, extracting mapping information from mysql and using perl but I have not got any luck. Would anyone please help me?

Answer 1

[MAPK]

This option should do the job in standalone blast program (first work it out for prot then nt):

blastdbcmd -db -entry_batch