[Boost-users] question on possible regex variants for sequence compares

From: Mike Marchywka (marchywka_at_[hidden])
Date: 2007-12-13 11:43:55

Hi,
This isn't boost-specific but the list seems reasonably tolerant of off-topic posts
and it does relate to the regex features. To cut to the chase, my question
is , " does boost implement anything that may help in searching an array of
strings for particular types of patterns?"

As I indicated earlier, I'm doing sequence alignments between many long
strings ( 5-50 strings, 10k-5M chars long, either DNA or proteins)
( to make this post informative for others that may be interested in algorithms, see things like this:
http://www.google.com/search?hl=en&q=%22sequence+alignment%22+site%3Aciteseer.ist.psu.edu&btnG=Search
)
Anyway, manually sorting through 5Meg string arrays is a bit tedious but I wanted to know if there are
particular ways of describing queries that may be similar to but faster than regex ( "show me
everyplace in this string alignment where 4 of the 5 characters are identical, but only where
5 or more characters meet this criterion?")

If you look at this ornately colored html, you can get some idea of what the data look like:

http://www.spottext.com/marchywka/some_dog_prosites.html

Besides queries on the character content, I'd be looking for similar patterns in the
"rules" locations( "show me every sequence where 4 of the 5 things match rule 234")

Ultimately, once I have some idea what is going on and have ad hoc tools for
debugging, I'd like to make an automated system and can write specialized code
but a general query system is great for survey and debug. 

Thanks.

Mike Marchywka
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