Selecting cDNA (IMAGE) clones by chromosomal position

Richard Williams rdwillia at hgmp.mrc.ac.uk
Tue Aug 7 08:05:24 EST 2001


Does anyone have any suggestions as to the 'best' method of selecting 
large numbers of IMAGE (cDNA) clones that map to specific chromosomal
regions? By 'region', I'm thinking in terms of entire cytogenetic bands,
rather than more specific loci. I'd obviously like comprehensive coverage
of these regions, while minimising needless duplication and spurious
matches, but I guess this will remain a non-trivial task until gene
numbers and positions are more precisely defined!


Some possible approaches:

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. Eliminate similar clones by UniGene
clustering..? Or maybe BLAST directly against UniGene seq.uniq FASTA
database & select IMAGE clones from 'positive' clusters?

2) Use radiation hybrid mapping & ePCR data in GeneMap99/MapGene.

3) Use reference intervals and FISH mapping data in UniGene.

4) Use BLAST mapping data in all_est.txt, cross-referenced with cytoband
file from UCSC Golden Path. Again, would have to cluster by some means
to reduce duplication, and set parameters carefully to reduce false
positives.

etc.

I'd much rather do this by setting up local databases that can be queried
with SQL or Perl scripts (as we're already doing with UniGene, GeneMap & 
some of the UCSC data), rather than clicking on websites several thousand 
times! But all suggestions are welcome.


Richard.




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