[Bioperl-l] experimental Bio::Search::Tiling implementation

[Mark A. Jensen]

[and here it is: http://bugzilla.bioperl.org/show_bug.cgi?id=2830 ]
----- Original Message ----- 
From: "Mark A. Jensen" <maj at fortinbras.us>
To: "Steve Chervitz" <sac at bioperl.org>; "BioPerl List" 
<bioperl-l at lists.open-bio.org>
Sent: Tuesday, May 19, 2009 7:16 PM
Subject: Re: [Bioperl-l] experimental Bio::Search::Tiling implementation


> Thanks Steve--great idea. It would be great if users who have had any issues 
> with Bioperl tiling (or any other algorithm, for that matter)
> on particular datasets would send them along. I will enter an enhancement bug 
> report for this purpose; folks can attach their problem data to it. MAJ
> (P.S. to all; there are also some rudimentary run tests at
> bioperl-dev/trunk/t/SearchIO/Tiling.t)
>
> ----- Original Message ----- 
> From: "Steve Chervitz" <sac at bioperl.org>
> To: "Mark A. Jensen" <maj at fortinbras.us>
> Cc: "BioPerl List" <bioperl-l at lists.open-bio.org>
> Sent: Tuesday, May 19, 2009 6:21 PM
> Subject: Re: [Bioperl-l] experimental Bio::Search::Tiling implementation
>
>
> Mark,
>
> Great work. My SearchUtils tiling function has been lingering for far
> too long (at least a decade).
>
> Your comment about BLASTP is fitting. I was working almost exclusively
> with BLASTP when developing the original tiling function and it seems
> like the trouble ensued when using it with other blast flavors. There
> was insufficient exploration of blast alignment edge cases. It would
> be good to come up with a comprehensive collection of blast reports to
> stress test your tiling impl. The set currently in t/data is a good
> start, but may not be sufficient.
>
> Cheers,
> Steve
>
> On Tue, May 19, 2009 at 12:31 PM, Mark A. Jensen <maj at fortinbras.us> wrote:
>> Hi All-
>>
>> With the frequent posts concerning HSP tilings, I thought it was time
>> to create the sought-after Bio::Search::Tiling namespace, and attempt
>> to provide a robust and exact tiling algorithm. I think it's timely,
>> too, since Jason's usual remarks involve the use of wu-blast with
>> the --links option, and wu-blast has recently turned commercial and
>> is evidently costly to obtain.
>>
>> The namespace includes an abstract interface B:S:Tiling::TilingI, and
>> a concrete class called B:S:Tiling::MapTiling. The object is
>> constructed like so
>>
>> $tiling = Bio::Search::Tiling::MapTiling($your_blast_hit);
>>
>> and provides methods for identities(), conserved(), and length();
>> other stats could also be provided. Identities and conserved sites are
>> correctly estimated, accounting for multiple overlapping HSPs. There
>> is also a method next_tiling($type), where $type is 'hit', 'subject'
>> (alias for 'hit'), or 'query', which an iterator stepping through all
>> minimal sets of HSPs that completely cover the 'hit' or 'query'
>> sequence. One feature is that the individual tilings do not need to be
>> generated to estimate the statistics; next_tiling provides the individual
>> tilings only if you want/need them.
>>
>> I've made it available in a pre-alpha state on bioperl-dev. It's
>> working and workable with plenty pod: see the synopses. It would
>> be excellent if interested folks would try it out on their favorite
>> data. Some niceties are not yet implemented, so BLASTP data is your
>> best bet for success. Check it out via svn into a separate working
>> directory, let me know if there are any questions.
>>
>> Below is table of comparison numbers using the current SearchUtils
>> tiling implementation and some of the new methods, on some test data
>> in t/data. Please see pod for many more details.
>>
>> Cheers,
>> Mark
>>
>>
>> *****
>> Comparision of methods with (patched) Bio::Search::SearchUtils
>> using test data t/data/dcr1_sp.WUBLASTP
>>
>> SU: SearchUtils
>> MT: MapTiling, using methods 'exact', 'est', 'max'
>> so MT(q:x) is MapTiling, stats calculated on the query, with the exact
>> method, etc.
>>
>> Identities
>> Hit SU MT(q:x) MT(q:e) MT(q:m) MT(s:x) MT(s:e) MT(s:m)
> ...
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>>
>
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