mapping oligo sequences to the genome

Model Organism: Worms WormBase
1

*** I figured this out using the ucsc BLAT search , but there seems to be an error with the BLAT searches via WormBase (see below). The ucsc BLAT search has a little note at the bottom of the search page pointing out how to retrieve the coordinates for a list of sequences. A note like this on the WormBase blat page would be great ***

Hi,
Is there a way find the genome coordinates for a list of oligo sequences? I looked at Worm Mart and Batch Sequences but they don’t seem to support this type of query. This is similar to my question a while back (where I had a list of oligo names and wanted to map them) but in this case I have the sequence and just need to get the chromosome locations). e-PCR doesn’t seem to do it. Would you know if there is any way to do this(maybe via BLAST)?
Kind Regards,
Lisa

** the wormbase C. elegans BLAT gives the following error:

An error occurred:

BLAST/BLAT search failed!

Couldn’t connect to localhost 2007
Connection refused
Sorry, the BLAT/iPCR server seems to be down. Please try again later.

2

Hi nemazur -

Thanks for the report!

I’ve fixed the problems with the blat server. I’ve also provided the exact same text as a note on the bottom of the page describing BLAT (it’s still on the development site at the moment but will be on wormbase.org in the next week or so.

Thanks again,

Todd

3

Thanks Todd, that’s great!
Lisa