Question: converting gene name to gene id
0
gravatar for Fereshteh
21 months ago by
Fereshteh2.7k
Fereshteh2.7k 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 • 1.0k views
ADD COMMENTlink modified 21 months ago by biocyberman640 • written 21 months ago by Fereshteh2.7k
2
gravatar for biocyberman
21 months ago by
biocyberman640
Denmark
biocyberman640 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 21 months ago • written 21 months ago by biocyberman640

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

ADD REPLYlink written 21 months ago by Fereshteh2.7k
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 21 months ago • written 21 months ago by biocyberman640

@Fereshteh See my update answer. 

ADD REPLYlink written 21 months ago by biocyberman640
1

thank you so much, for your complete explanation   

ADD REPLYlink modified 21 months ago • written 21 months ago by Fereshteh2.7k
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