[BioPython] help for searching overlapping occurrences

[Harry Mangalam]

I thought you were looking for a Python lib, so I didn't respond.

If interested, you're welcome to a newer version.  It depends on what kind of 
thing you're looking for.  If a Python module for doing this, then no. If very 
long patterns, probably not - tacg only supports ~50 bp patterns as supplied 
(altho you could recompile to extend this arbitrarily I guess). If you're 
looking for a standalone app to do it, yes.

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It supports IUPAC patterns, regexes, TRANSFAC matrices, and rules (logical 
combinations of the previous patterns as in (pattern_A AND pattern_B AND 
pattern_C) NOT ((Pattern_D AND pattern_E) XOR (pattern_F OR patternG)) in a 
sliding window of XX bases (useful for finding things like SARS/MARS)

Both strands at the same time, auto sequence conversion on input, no limit to 
sequence length, 30-50x faster than the GCG equivs, 100x more memory efficient 
than the EMBOSS equivs, (but overall less functionality - only nucleic acid 
searches supported currently)
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Sebastian Bassi wrote:
> Alessandro wrote:
> 
>> I' am looking for a method like finditer from module re but returning 
>> all the occurrences of a pattern in a straing even if overlapping to 
>> each other. Thanks a lot.
>> Alessandro Coppe
> 
> 
> You may try this:
> 
> e-Paper:
> tacg, a grep for DNA (Harry J Mangalam).
> BMC Bioinformatics 2002, 3:8.
> http://www.biomedcentral.com/1471-2105/3/8
> Software:
> http://tacg.sourceforge.net
> 
> I never used this program but it seems it could be useful for this kind
> of job.
> 
> 

-- 
Cheers, Harry
Harry J Mangalam - 949 856 2847 (v&f) - hjm at tacgi.com
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