converting gene name to gene id

Question

[zizigolu]

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

Answer 1

[biocyberman]

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 from here

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
   

[zizigolu]

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

[biocyberman]

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

[biocyberman]

@Fereshteh See my updated answer.

[zizigolu]

thank you so much, for your complete explanation