[Biojava-l] BlastLikeAlignment with BlastLikeSearchBuilder

[Keith James]

>>>>> "Max" == Markus Roth <Markus.Roth@tg.fh-giessen.de> writes:

    Max> hi there, I've been trying to create
    Max> SeqSimilaritySearchResults from SAX with the
    Max> BlastLikeSearchBuilder. Is there any possibility to get the
    Max> MatchConsensus from the Alignment ?  or is there nothing
    Max> about the Consensus in the SeqSimilaritySearchHit
    Max> (SeqSimilaritySearchSubHit) ?  I found something like this in
    Max> Blast2HTMLHandler --> BlastLikeAlignment, how can I get this
    Max> with the SeqSimilarityAdapter ?

    Max> regards Max

Hi,

The short answer is that the only alignment information retained by a
SeqSimilaritySearchSubHit is the Alignment object itself.

The long answer is that there are two main parts to the blast/fasta
handling code; the parser, which passes on absolutely all the
information in the blast reports as SAX events and the handlers, which
interpret some (or all) of the events. Not all handlers will use all
the events and the current BlastLikeSearchBuilder ignores the
MatchConsensus data, mainly because the SeqSimilaritySearch object
model is quite restricted. The Blast2HTMLHandler uses all the SAX
events, which is why you can see the MatchConsensus in its output.

This is something which could be changed if there is the
demand. Perhaps the SeqSimilaritySearch interfaces could be richer?
Does anyone on the mailing list have opinions on this?

Keith

-- 

- Keith James <kdj@sanger.ac.uk> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -