Selecting cDNA (IMAGE) clones by chromosomal position

Richard Williams rdwillia at hgmp.mrc.ac.uk
Wed Aug 8 10:17:25 EST 2001


In article <3B710932.321B68BA at bbsrc.ac.uk>,
Simon Andrews  <simon.andrews at bbsrc.ac.uk> wrote:
>Richard Williams wrote:
>> 
>> Does anyone have any suggestions as to the 'best' method of selecting
>> large numbers of IMAGE (cDNA) clones that map to specific chromosomal
>> regions? 
>>
>> 1) Select clones based on sequence similarities to known genes in
>> ENSEMBL, perhaps by BLASTing EST databases with ENSEMBL cDNAs from the
>> region of interest as queries.
>
>I believe the latest release of Ensembl has ESTs mapped to it already. 
>You could probably just mirror their MySQL database and use that
>information to get the ESTs in a particular location.  You would need to
>subselect for IMAGE clones, but that shouldn't be too hard (easy to say
>when you don't have to do it!).

Thanks, this looks like a possibility. I've just been reading some of the
ENSEMBL docs, & there are some nice bioperl objects with associated
methods that can be used to query the database directly (either a local
mirror or a public MySQL server at Sanger). It looks like I have a fair
bit of reading to do! It may well be possible to extract only those ESTs
which overlap with confirmed ENSEMBL exons in the regions of interest
(there's certainly an 'overlaps' method for sequence features), though
it's been suggested to me elsewhere that this approach may be
too limiting. The UCSC all_est file also has direct EST -> chromosome
bp mapping. One significant problem with using either database would be
knowing what to throw away (is it appropriate to use UniGene to cluster
the mapped ESTs, or is there a better way of reducing the numbers of 
redundant clones, perhaps using the mapped positions to detect
overlap..?). This sort of thing is quite easy to do semi-manually
(e.g. using the ENSEMBL website or UCSC browser), but that isn't so
practical for larger regions. Again, suggestions are welcome!


Richard.    




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