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

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

       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 v5.32.0			  2002-02-04		     Boulder::Blast(3)

NAME | SYNOPSIS | DESCRIPTION | METHODS | TAGS | CAVEATS | SEE ALSO | AUTHOR | EXAMPLE BLASTN RUN | Example BLASTP run

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