Many genomic sequences exist (albeit temporarily) in the nucleotide
databases as collections of unordered non-overlapping contigs.
It strikes me that by aligning pre-existing cDNA sequences to the draft
genomic sequence, would in a lot of cases determine the order of the
non-overlapping segments. Obviously the longer the cDNA sequences, the more
effective the strategy, I have been able to do this myself in a number of
cases by using long cDNA sequences from the Kazusa Human cDNA Project
(KIAA...)
If this approach could be generally implemented before data is submitted,
it would improve the usability of the draft genomic sequence (ie with
'est_genome') and may in some cases speed up final finishing to contiguous
sequence.
Jeffrey Keen
Molecular Medicine Unit
University of Leeds
