Question: converting gene name to gene id
0
gravatar for F
2.6 years ago by
F3.1k
Iran
F3.1k wrote:

hi,

i found many tools for ID conversion but i found no one to convert gene name to gene ID for example FLP1 (gene name) to R0010W (gene ID).

do you know such a tool please?

thank you

myposts gene • 1.7k views
ADD COMMENTlink modified 2.6 years ago by biocyberman700 • written 2.6 years ago by F3.1k
3
gravatar for biocyberman
2.6 years ago by
biocyberman700
Denmark
biocyberman700 wrote:

IDs are databse specific. Can you tell which database you want to have IDs from (i.e. genbank, ensemble, etc)?

This http://biodb.jp/#ids may be want you want to use, but it does not work right now. Or try playing around with ENSEML biomart http://www.ensembl.org/biomart/martview

 

Update:

Assume you are working with the Yeast database (because the ID you gave as an example is from here: http://www.yeastgenome.org/locus/S000029654/overview

So do the following: 

1. Download this cross reference file:

http://downloads.yeastgenome.org/curation/chromosomal_feature/dbxref.tab

2. Put all your genes in a file called mygenes.txt in one column, for example:

 FLP1
 CKS1
 GCN4
 PAP1

 

3. Make sure dbxref.tab and mygenes.txt are in the same folder. Run this (in a linux machine):

gawk 'BEGIN{FS="\t"}(NR == FNR){a[$1]++;next}{ if ($6 in a) print $4"\t"$6}' mygenes.txt dbxref.tab |sort|uniq

 

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by biocyberman700

thank you, actually i don't know which database i want, i only know about needing conversion

ADD REPLYlink written 2.6 years ago by F3.1k
1

That is very challenging :-) Try to retrieve information from this file maybe: http://downloads.yeastgenome.org/curation/chromosomal_feature/dbxref.tab

README of the file: http://downloads.yeastgenome.org/curation/chromosomal_feature/dbxref.README

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by biocyberman700

@Fereshteh See my update answer. 

ADD REPLYlink written 2.6 years ago by biocyberman700
1

thank you so much, for your complete explanation   

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by F3.1k
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: 1020 users visited in the last hour