How to retrieve gene symbols with refseq protein accesion number or gi number?
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9.1 years ago
grayapply2009 ▴ 300

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?

mysql perl • 2.4k views
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9.1 years ago
MAPK ★ 2.1k

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

blastdbcmd -db -entry_batch
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