What are the existing toolkits / webservices out there that can be
used for genomic sequence search and analysis? What are the copyright
terms on the code, if any is available (any under GPL?)

Caveat:  'homolog finding' toolkits akin to BLAST and HMM are of no
interest, i.e. one should be able to do a 'unrestricted brute force'
search for all occurences of any genetic sequence, no matter how short
a sequence is
and not neccesarily comprising a gene, in a given publically available
genome (Homo Sapience, Mus Musculus, etc.) or in user-supplied data,
and get detailed results -- all locations of matches,
overlapping/non-overlapping matches, location of matches relative to
open reading frames, location of mathes on/before/after/ known genes,
location of matches relative to previous search matches, and other
statistical data. Same for comparison of mutliple search results and
'sub-searches' within set of matches for previous searches.

Does anything like this exist out there? Is anyone working on it? (And
if they are, are they looking for contributors? :))

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Request for Question Clarification by omniscientbeing-ga on 07 Oct 2002 23:15 PDT

By "existing toolkit/webservices" do you mean all such products--free
or by subscription or sale only? i.e., are you interested in the web
services offered by genomics companies such as Celera, or only in
commercial applications that are either freeware or priced for
individual/academic use?

~omnicientbeing-ga

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Clarification of Question by oy_such_mishu-ga on 08 Oct 2002 13:08 PDT

I am interested in all such products, however I believe that high-end
'suites' of products that require a meeting with a sales rep would be
pretty tough to research. :) Also, I am more interested in products
that focus exactly on the task of interest, versus offerings like
Celera's, which *might* include this functionality, but only when
searching through their own data.My understanding is that products
like that are primarily a vehicle for their own genomic data and not a
tool designed to work with public domain genomes and/or uploaded
user's data. As usual, I might be very wrong. :)

Thanks!

The Univ. of Maryland is the place to ask- unless you're from UMCP.