[Bioclusters] Blast Source

[Elia Stupka]

> A colleague of mine is trying to use blast to determine very loose 
> matches.

The other important question is what exactly is he trying to do? In 
other words, what does he mean exactly by "loose matches" and what sort 
of sequences is he comparing. Many people talk about loose matches not 
because they are looking for long not-well conserved sequences but 
because they are trying to search for short well-conserved sequences in 
a long sea of non-conservation. In that case something like 
promoterwise (http://www.ebi.ac.uk/Wise2/promoterwise.html) would be 
more interesting than BLAST, or even some of the motif-findin 
algorithms like meme and footprinter, if it is a recurring motif...

Elia

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Temasek Life Sciences Laboratory
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