Boulder::Blast(3pm)					User Contributed Perl Documentation				       Boulder::Blast(3pm)

NAME

       Boulder::Blast - Parse and read BLAST files

SYNOPSIS

	 use Boulder::Blast;

	 # parse from a single file
	 $blast = Boulder::Blast->parse('run3.blast');

	 # parse and read a set of blast output files
	 $stream = Boulder::Blast->new('run3.blast','run4.blast');
	 while ($blast = $stream->get) {
	    # do something with $blast object
	 }

	 # parse and read a whole directory of blast runs
	 $stream = Boulder::Blast->new(<*.blast>);
	 while ($blast = $stream->get) {
	    # do something with $blast object
	 }

	 # parse and read from STDIN
	 $stream = Boulder::Blast->new;
	 while ($blast = $stream->get) {
	    # do something with $blast object
	 }

	 # parse and read as a filehandle
	 $stream = Boulder::Blast->newFh(<*.blast>);
	 while ($blast = <$stream>) {
	    # do something with $blast object
	 }

	 # once you have a $blast object, you can get info about it:
	 $query = $blast->Blast_query;
	 @hits	= $blast->Blast_hits;
	 foreach $hit (@hits) {
	    $hit_sequence = $hit->Name;    # get the ID
	    $significance = $hit->Signif;  # get the significance
	    @hsps = $hit->Hsps; 	   # list of HSPs
	    foreach $hsp (@hsps) {
	      $query   = $hsp->Query;	   # query sequence
	      $subject = $hsp->Subject;    # subject sequence
	      $signif  = $hsp->Signif;	   # significance of HSP
	    }
	 }

DESCRIPTION

       The Boulder::Blast class parses the output of the Washington University (WU) or National Cenber for Biotechnology Information (NCBI) series
       of BLAST programs and turns them into Stone records.  You may then use the standard Stone access methods to retrieve information about the
       BLAST run, or add the information to a Boulder stream.

       The parser works equally well on the contents of a static file, or on information read dynamically from a filehandle or pipe.

METHODS

   parse() Method
	   $stone = Boulder::Blast->parse($file_path);
	   $stone = Boulder::Blast->parse($filehandle);

       The parse() method accepts a path to a file or a filehandle, parses its contents, and returns a Boulder Stone object.  The file path may be
       absolute or relative to the current directgly.  The filehandle may be specified as an IO::File object, a FileHandle object, or a reference
       to a glob ("*FILEHANDLE" notation).  If you call parse() without any arguments, it will try to parse the contents of standard input.

   new() Method
	   $stream = Boulder::Blast->new;
	   $stream = Boulder::Blast->new($file [,@more_files]);
	   $stream = Boulder::Blast->new(*FILEHANDLE);

       If you wish, you may create the parser first with Boulder::Blast new(), and then invoke the parser object's parse() method as many times as
       you wish to, producing a Stone object each time.

TAGS

       The following tags are defined in the parsed Blast Stone object:

   Information about the program
       These top-level tags provide information about the version of the BLAST program itself.

       Blast_program
	   The name of the algorithm used to run the analysis.	Possible values include:

		   blastn
		   blastp
		   blastx
		   tblastn
		   tblastx
		   fasta3
		   fastx3
		   fasty3
		   tfasta3
		   tfastx3
		   tfasty3

       Blast_version
	   This gives the version of the program in whatever form appears on the banner page, e.g. "2.0a19-WashU".

       Blast_program_date
	   This gives the date at which the program was compiled, if and only if it appears on the banner page.

   Information about the run
       These top-level tags give information about the particular run, such as the parameters that were used for the algorithm.

       Blast_run_date
	   This gives the date and time at which the similarity analysis was run, in the format "Fri Jul  6 09:32:36 1998"

       Blast_parms
	   This points to a subrecord containing information about the algorithm's runtime parameters.	The following subtags are used.  Others
	   may be added in the future:

		   Hspmax	   the value of the -hspmax argument
		   Expectation	   the value of E
		   Matrix	   the matrix in use, e.g. BLOSUM62
		   Ctxfactor	   the value of the -ctxfactor argument
		   Gapall	   The value of the -gapall argument

   Information about the query sequence and subject database
       Thse top-level tags give information about the query sequence and the database that was searched on.

       Blast_query
	   The identifier for the search sequence, as defined by the FASTA format.  This will be the first set of non-whitespace characters
	   following the ">" character.  In other words, the search sequence "name".

       Blast_query_length
	   The length of the query sequence, in base pairs.

       Blast_db
	   The Unix filesystem path to the subject database.

       Blast_db_title
	   The title of the subject database.

   The search results: the Blast_hits tag.
       Each BLAST hit is represented by the tag Blast_hits.  There may be zero, one, or many such tags.  They will be presented in reverse sorted
       order of significance, i.e. most significant hit first.

       Each Blast_hits tag is a Stone subrecord containing the following subtags:

       Name
	   The name/identifier of the sequence that was hit.

       Length
	   The total length of the sequence that was hit

       Signif
	   The significance of the hit.  If there are multiple HSPs in the hit, this will be the most significant (smallest) value.

       Identity
	   The percent identity of the hit.  If there are multiple HSPs, this will be the one with the highest percent identity.

       Expect
	   The expectation value for the hit.  If there are multiple HSPs, this will be the lowest expectation value in the set.

       Hsps
	   One or more sub-sub-tags, pointing to a nested record containing information about each high-scoring segment pair (HSP).  See the next
	   section for details.

   The Hsp records: the Hsps tag
       Each Blast_hit tag will have at least one, and possibly several Hsps tags, each one corresponding to a high-scoring segment pair (HSP).
       These records contain detailed information about the hit, including the alignments.  Tags are as follows:

       Signif
	   The significance (P value) of this HSP.

       Bits
	   The number of bits of significance.

       Expect
	   Expectation value for this HSP.

       Identity
	   Percent identity.

       Positives
	   Percent positive matches.

       Score
	   The Smith-Waterman alignment score.

       Orientation
	   The word "plus" or "minus".	This tag is only present for nucleotide searches, when the reverse complement match may be present.

       Strand
	   Depending on algorithm used, indicates complementarity of match and possibly the reading frame.  This is copied out of the blast
	   report.  Possibilities include:

	    "Plus / Minus" "Plus / Plus" -- blastn algorithm
	    "+1 / -2" "+2 / -2" 	-- blastx, tblastx

       Query_start
	   Position at which the HSP starts in the query sequence (1-based indexing).

       Query_end
	   Position at which the HSP stops in the query sequence.

       Subject_start
	   Position at which the HSP starts in the subject (target) sequence.

       Subject_end
	   Position at which the HSP stops in the subject (target) sequence.

       Query, Subject, Alignment
	   These three tags contain strings which, together, create the gapped alignment of the query sequence with the subject sequence.

	   For example, to print the alignment of the first HSP of the first match, you might say:

	     $hsp = $blast->Blast_hits->Hsps;
	     print join("
",$hsp->Query,$hsp->Alignment,$hsp->Subject),"
";

       See the bottom of this manual page for an example BLAST run.

CAVEATS

       This module has been extensively tested with WUBLAST, but very little with NCBI BLAST.  It probably will not work with PSI Blast or other
       variants.

       The author plans to adapt this module to parse other formats, as well as non-BLAST formats such as the output of Fastn.

SEE ALSO

       Boulder, Boulder::GenBank

AUTHOR

       Lincoln Stein <lstein@cshl.org>.

       Copyright (c) 1998-1999 Cold Spring Harbor Laboratory

       This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.  See DISCLAIMER.txt for
       disclaimers of warranty.

EXAMPLE BLASTN RUN

       This output was generated by the quickblast.pl program, which is located in the eg/ subdirectory of the Boulder distribution directory.	It
       is a typical blastn (nucleotide->nucleotide) run; however long lines (usually DNA sequences) have been truncated.  Also note that per the
       Boulder protocol, the percent sign (%) is escaped in the usual way.  It will be unescaped when reading the stream back in.

	Blast_run_date=Fri Nov	6 14:40:41 1998
	Blast_db_date=2:40 PM EST Nov 6, 1998
	Blast_parms={
	  Hspmax=10
	  Expectation=10
	  Matrix=+5,-4
	  Ctxfactor=2.00
	}
	Blast_program_date=05-Feb-1998
	Blast_db= /usr/tmp/quickblast18202aaaa
	Blast_version=2.0a19-WashU
	Blast_query=BCD207R
	Blast_db_title= test.fasta
	Blast_query_length=332
	Blast_program=blastn
	Blast_hits={
	  Signif=3.5e-74
	  Expect=3.5e-74,
	  Name=BCD207R
	  Identity=100%25
	  Length=332
	  Hsps={
	    Subject=GTGCTTTCAAACATTGATGGATTCCTCCCCTTGACATATATATATACTTTGGGTTCCCGCAA...
	    Signif=3.5e-74
	    Length=332
	    Bits=249.1
	    Query_start=1
	    Subject_end=332
	    Query=GTGCTTTCAAACATTGATGGATTCCTCCCCTTGACATATATATATACTTTGGGTTCCCGCAA...
	    Positives=100%25
	    Expect=3.5e-74,
	    Identity=100%25
	    Query_end=332
	    Orientation=plus
	    Score=1660
	    Strand=Plus / Plus
	    Subject_start=1
	    Alignment=||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...
	  }
	}
	=

Example BLASTP run
       Here is the output from a typical blastp (protein->protein) run.  Long lines have again been truncated.

	Blast_run_date=Fri Nov	6 14:37:23 1998
	Blast_db_date=2:36 PM EST Nov 6, 1998
	Blast_parms={
	  Hspmax=10
	  Expectation=10
	  Matrix=BLOSUM62
	  Ctxfactor=1.00
	}
	Blast_program_date=05-Feb-1998
	Blast_db= /usr/tmp/quickblast18141aaaa
	Blast_version=2.0a19-WashU
	Blast_query=YAL004W
	Blast_db_title= elegans.fasta
	Blast_query_length=216
	Blast_program=blastp
	Blast_hits={
	  Signif=0.95
	  Expect=3.0,
	  Name=C28H8.2
	  Identity=30%25
	  Length=51
	  Hsps={
	    Subject=HMTVEFHVTSQSW---FGFEDHFHMIIR-AVNDENVGWGVRYLSMAF
	    Signif=0.95
	    Length=46
	    Bits=15.8
	    Query_start=100
	    Subject_end=49
	    Query=HLTQD-HGGDLFWGKVLGFTLKFNLNLRLTVNIDQLEWEVLHVSLHF
	    Positives=52%25
	    Expect=3.0,
	    Identity=30%25
	    Query_end=145
	    Orientation=plus
	    Score=45
	    Subject_start=7
	    Alignment=H+T + H	  W    GF   F++ +R  VN + + W V ++S+ F
	  }
	}
	Blast_hits={
	  Signif=0.99
	  Expect=4.7,
	  Name=ZK896.2
	  Identity=24%25
	  Length=340
	  Hsps={
	    Subject=FSGKFTTFVLNKDQATLRMSSAEKTAEWNTAFDSRRGFF----TSGNYGL...
	    Signif=0.99
	    Length=101
	    Bits=22.9
	    Query_start=110
	    Subject_end=243
	    Query=FWGKVLGFTL-KFNLNLRLTVNIDQLEWEVLHVSLHFWVVEVSTDQTLSVE...
	    Positives=41%25
	    Expect=4.7,
	    Identity=24%25
	    Query_end=210
	    Orientation=plus
	    Score=65
	    Subject_start=146
	    Alignment=F GK   F L K    LR++	EW     S   +	 T     +...
	  }
	}
	=

perl v5.10.1							    2002-02-04						       Boulder::Blast(3pm)