We are interested in searching specific sequence data bases (an example
would be haemophilus influenzae) for short sequences (say TA repeats).
So far, I have run into several problems. 1) most sequence databases will
not let you pick a specific entry or organism and 2) when dealing with such
short sequences (say 20 bases) the results are usually below the cutoff
and produce no results. The TIGR database and European databases for H.flu
contain the entire 1.8 million base sequence but don't allow searches of
this size. The current BLAST system doesn't let you choose what you want
to search.
Is anyone aware of a method/program that could be used to perform such a search?
The only thing that I have been able to come up with is to cut the H flu
sequence into little pieces and do the analysis on my lab computer. There
must be another way.
Thanks for any help
Mike
--
Michael Gorry
mcgorry at med.pitt.edu
