Question: How to retrieve gene symbols with refseq protein accesion number or gi number?
0
gravatar for grayapply2009
3.9 years ago by
grayapply2009170
United States
grayapply2009170 wrote:

I have about 70,000 refseq protein accesion 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: C: How to get protein names, gene symbols, refseq numbers, gi numbers... using UCSC 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 id gene symbol perl gene • 1.3k views
ADD COMMENTlink modified 3.9 years ago by MAPK1.4k • written 3.9 years ago by grayapply2009170
0
gravatar for MAPK
3.9 years ago by
MAPK1.4k
United States
MAPK1.4k wrote:

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

blastdbcmd -db -entry_batch

 

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by MAPK1.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1556 users visited in the last hour