[Biojava-l] Biojava-l Digest, Vol 131, Issue 3

[Peter S]

Thanks Andreas, 

I am switching from python/perl so my java is not great but with the implementation you mention I would need to pass the sequence each time and run it one by one? SSEARCH is also 'slow' (SW) but has a lot of optimization in place so at the end it does not take that long to run it. It's in C++ though.

Peter



On Friday, 17 January 2014, 18:09, Andreas Prlic <andreas at sdsc.edu> wrote:
 
We do have a Smith Waterman implementation in Biojava. However the algorithm is based on dynamic programming, which by definition is "slow" but gives you the optimal alignment...

http://biojava.org/wiki/BioJava:CookBook3:PSA#Local_alignment


Andreas







On Fri, Jan 17, 2014 at 9:50 AM, Peter S <peters337 at yahoo.co.uk> wrote:

Thanks, I will give it a try. 
>
>Does it mean there is no fast implementation of SW in java that I can use? 
>
>Best,
>Peter
>
>
>
>
>On Friday, 17 January 2014, 17:45, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:
>
>Hi Peter,
>
>give it a try with Levenshtein Distance. You can use StringUtils from apache common lang. it has a getLevenshteinDistance method.
>
>best,
>
>Khalil
>
>
>
>On 17 Jan 2014, at 18:37, Peter S <peters337 at yahoo.co.uk> wrote:
>
>Hi Khalil,
>>
>>
>>By short sequence I mean 12-18 nt long. I need to make alignment against the entire transcriptome and detect matches with up to 3 mismatches. This is the reason I need something quite fast but sensitive at the same time. 
>>
>>
>>Many thanks,
>>Peter
>>
>>
>>
>>On Friday, 17 January 2014, 17:26, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:
>>
>>Hi,
>>
>>what do you mean by short sequences? NT or AA?
>>
>>Best
>>
>>Khalil
>>
>>On 17 Jan 2014, at 18:00, biojava-l-request at lists.open-bio.org wrote:
>>
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>>> Today's Topics:
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>>>   1. Database search with Smith and Waterman (Peter S)
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>>> ----------------------------------------------------------------------
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>>> Message: 1
>>> Date: Fri, 17 Jan 2014 13:27:17 +0000 (GMT)
>>> From: Peter S <peters337 at yahoo.co.uk>
>>> Subject: [Biojava-l] Database search with Smith and Waterman
>>>
> To: "biojava-l at lists.open-bio.org" <biojava-l at lists.open-bio.org>
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>>> Dear All,?
>>>
>>> I'm looking for an implementation of Smith and Waterman algorithm to use in the Java desktop application I want to develop.?
>>>
>>> I did find some information on pairwise aligners but what I would ideally want to have is something similar to the SSEARCH package that can perform alignments against a very big databases,
> saved locally in a fasta format. Speed is quite important and ideally I would need an output that I can easily parse, identifying mismatch/gap positions etc.
>>>
>>> Any suggestions if there is any java implementation that would fit the description? I will be working on short sequences so sensitivity is crucial.?
>>>
>>> Thanks very much for your help,
>>> Peter
>>>
>>>
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