how to mapp ensembl to refseq?

[floh]

Hey everyone!

I need to mapp ensembl transcript identifiers(ENSMUST) to refseq
transcript identifiers(NM) for mouse. After a week of unsuccessful
mapping i searched in the internet for a HowTo and found this google
group ;)

i read some discussions and discovered that there is this GenMAPP
database which i could use. unfortunately i can not find the database
features which leads to my first question:

1. is it even possible to mapp ensembl to refseq using the GenMAPP
database?


2. a try to download the database did not work as well (is www.genmapp.org
the right URL for download?) because the website is unable to connect.


3. in the FAQ i read that the database is only available for windows
systems. I am not very glad about this fact because i work on a unix
system using a mysql server.

i thougth that it might be possible to offer me a mysql database
backup for download?

thanks for your answers!
floh

[Alexander Pico]

Hi Floh,

We currently get almost all our mappings from Ensembl now, via their Perl
API. We then transform and load it into out our MySQL databases from which
we generate our Access and Derby databases.

So, the best way to get the most up-to-date specific mappings is to go to
Ensembl directly. I recommend the BioMart tool:
http://www.ensembl.org/biomart/martview/

They might not have exactly what you want, however (in which case, neither
do we). Ensembl maps external references (Xrefs) to their gene-level
objects (ENSMUSG) which are in turn mapped to transcripts (ENSMUST). They do
not provide direct mappings from transcripts to Xrefs. So, you would end up
with a list of transcripts related to a gene and a list of refseq IDs
related to a gene, but not a mapping from refseq to transcripts.

I do not know where to get that mapping.

-Alex

On 5/28/08 7:03 AM, "floh" <florian.teich...@googlemail.com>
wrote: