Converting a list of different gene names to a common name in order to retrieve sequence data

Question

[nathanielsaxe]

I am trying to retrieve the mRNA sequence for a bunch of different genes, but the list I got given is a mixture of different gene names. Is there a website that can convert different gene ids to one particular type or a website that can accept different gene ids and give me a list of mRNAs/UTRs etc.

A sample of the list I have:

vab-10
vig-1
T06D8.1
sca-1
cyc-2.1
unc-44
F01G4.6
cfz-2
W06H8.5
alh-4
dlg-1
CELE_F59B2.13
R166.6
Y51F10.12
F32B5.10
C45E1.8
F25F1.4
B0041.10
D2030.14
CELE_C27C7.12
CELE_C27C7.10
CELE_Y47H9C.19

Thanks

Answer 1

[michael.ante]

You can use ENSEMBL's biomart. Select your organism and the output fields (Associated Gene Name in your case). You can paste your list or upload it as text file for filtering ("Input external references ID list").

[Emily]

That won't work. To convert gene names using BioMart they must all be the same type to start with. If this list is a mixed selection of names it can't do it.

[michael.ante]

It will need a little bit of fiddling around, e.g. sorting the gene names according to the source and splitting the data base requests while selecting the filter correctly.

Alternatively, you can use the FireFox PlugIn BioBar to streamline your database requests.

[nathanielsaxe]

Just to clarify, that list is all I have, I don't have any more information on the source. I was hoping that there might be a something that'll look through all the different reference ids or something and output them in a common format.

[Emily]

Find the person who made the list and decided it was a good idea to list a bunch of IDs from different sources without listing the source, and send them a strongly worded email.

[cdsouthan]

This same person will have introduced errors in this listing anyway, so keep the email polite but just add "Emily says there must be a more precise way of doing this" (use Wormbase?)

Answer 2

[Prakki Rama]

Is this something you wanted?

NO.  QUERY     SYMBOL    ID        NAME    SPECIES
1    vab-10    vab-10    173058    VAB-10  nematode
2    vig-1     vig-1     173512    VIG-1   nematode
3    sca-1     sca-1     176512    SCA-1   nematode

Try using BioGPS.