TAGS USED IN BOULDER REPRESENTATION OF BLAST/FAST OUTPUT
			    July 28, 1998
			   Lincoln D. Stein

Last modified: November 6, 1998

INTRODUCTION
------------

The boulder format is used by the quickblast program and other tools
to run and parse the output of the BLAST and FAST family of sequence
similarity searching tools.  This document describes the tags that are
expected in the boulder stream from BLAST and BLAST-like searches.

DEFINED TAGS
------------

1. Information about the program

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.

2. Information about the run

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

3. Information about the query sequence and subject database

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.

Blast_db
	Unix filesystem path to the subject database.

Blast_db_title
	The title of the subject database.

4. The search results

Blast_hits
	This represents a list of BLAST (or FAST) hits on the query
	sequence.  There may be zero, one, or many such tags, each
	one corresponding to a hit on the subject database.  Each of
	these tags will contain one or more Hsp (high-scoring segment
	tags). 

	Blast_hits points to a boulder subrecord containing the
	following subtags:

	Name	The name 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 section (5) below.

5. The Hsp records

Each Blast_hit tag will have at least one, and possibly several Hsp
tags, each 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
	"plus" or "minus", only present for nucleotide matches

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.

EXAMPLES
--------

1. A BLASTN run

Here is the output from a typical blastn (nucleotide->nucleotide)
run.  Long lines have been truncated.  Note also that the percent sign 
(%) is escaped in the usual way.  It will be unescaped when reading
the boulder 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=||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...
  }
}
=

2. A 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     +...
  }
}
Blast_hits={
  Signif=0.99
  Expect=4.9,
  Name=F15H9.1
  Identity=31%25
  Length=426
  Hsps={
    Subject=LTLFIWIIACGFNNTQPLSYEENIQRLESCGKILPEESSNSITKSKYF...
    Signif=0.99
    Length=66
    Bits=23.2
    Query_start=141
    Subject_end=77
    Query=VSLHFWVVEVSTDQT--LSVENGIRRIHS-SLILSSITNQSFSVSESDKR...
    Positives=45%25
    Expect=4.9,
    Identity=31%25
    Query_end=206
    Orientation=plus
    Score=66
    Subject_start=4
    Alignment=++L  W++    + T  LS E  I+R+ S   IL   ++ S + S+...
  }
}
Blast_hits={
  Signif=0.99
  Expect=5.3,
  Name=D1007.9
  Identity=19%25
  Length=160
  Hsps={
    Subject=DFEIGILEKGFWAALRENTNVQQKFEITDRKMHNFMIFTAEKLKKKN...
    Signif=0.99
    Length=78
    Bits=21.1
    Query_start=135
    Subject_end=129
    Query=EWEVLHVSLHFWV-VEVSTDQTLSVENGIRRIHSSLILSS--ITNQSFS...
    Positives=51%25
    Expect=5.3,
    Identity=19%25
    Query_end=212
    Orientation=plus
    Score=60
    Subject_start=49
    Alignment=++E+  +   FW  +  +T+     E   R++H+ +I ++  +  +...
  }
}
Blast_hits={
  Signif=9999
  Expect=5.5,
  Name=T08E11.4
  Identity=36%25
  Length=299
  Hsps={
    Subject=LDSPCTETMNQKTFMLNHTVQNVSNIKERGIYTTNVE
    Length=36
    Bits=18.0
    Query_start=22
    Subject_end=165
    Query=IESTTTQVENQDVFFLTLLVQTVSN-GSGGRFVNNTQ
    Positives=48%25
    Expect=5.5,
    Identity=35%25
    Query_end=57
    Orientation=plus
    Score=51
    Subject_start=129
    Alignment=++S  T+  NQ  F L   VQ VSN    G +  N +
  }
  Hsps={
    Subject=LQCEKKHFDSKDWSIEVELVLTLKSSNG-QRL--SFTASSTLNEPA...
    Length=55
    Bits=17.2
    Query_start=134
    Subject_end=239
    Query=LEWEVLHVSLHFWVVEVSTDQTLSVENGIRRIHSSLILSSITNQSFSV...
    Positives=45%25
    Expect=5.5,
    Identity=36%25
    Query_end=188
    Orientation=plus
    Score=49
    Subject_start=187
    Alignment=L+ E  H     W +EV    TL   NG +R+  S   SS  N+...
  }
}
Blast_hits={
  Signif=1.00
  Expect=6.4,
  Name=K03H1.7
  Identity=22%25
  Length=88
  Hsps={
    Subject=MGQSFSSSFNAKQTSSSTPQKSTKTPTCSDPRSPSQDIERTPIQVK...
    Signif=1.00
    Length=84
    Bits=18.7
    Query_start=1
    Subject_end=88
    Query=MGVT-SGGLNFKDTVFNEQQRDIESTTT---QVENQDVFFLTLLVQTVS...
    Positives=44%25
    Expect=6.4,
    Identity=22%25
    Query_end=84
    Orientation=plus
    Score=53
    Subject_start=1
    Alignment=MG + S   N K T  +  Q+  ++ T    +  +QD+    + V...
  }
}
Blast_hits={
  Signif=1.00
  Expect=8.3,
  Name=Y67D8A_380.c
  Identity=41%25
  Length=47
  Hsps={
    Subject=TLLDAVSSDGSGADVEASGEDVQT
    Signif=1.00
    Length=24
    Bits=14.4
    Query_start=38
    Subject_end=44
    Query=TLLVQTVSNGSGGRFVNNTQDIQT
    Positives=58%25
    Expect=8.3,
    Identity=41%25
    Query_end=61
    Orientation=plus
    Score=41
    Subject_start=21
    Alignment=TLL    S+GSG     + +D+QT
  }
}
Blast_hits={
  Signif=1.00
  Expect=8.9,
  Name=C06A5.2
  Identity=26%25
  Length=214
  Hsps={
    Subject=TSGKKNKYKFKYGQIDQQELSINNDKTEYLENAQ---LTKLMSHADVR...
    Signif=1.00
    Length=100
    Bits=21.1
    Query_start=4
    Subject_end=207
    Query=TSGGLN---FKDTVFNEQQRDIESTTTQ-VENQDVFFLTLLVQ--TVSNG...
    Positives=50%25
    Expect=8.9,
    Identity=26%25
    Query_end=103
    Orientation=plus
    Score=60
    Subject_start=106
    Alignment=TSG  N   FK    ++Q+  I +  T+ +EN     LT L+    V...
  }
}
Blast_hits={
  Signif=1.00
  Expect=9.5,
  Name=Y71F9B_275.b
  Identity=26%25
  Length=264
  Hsps={
    Subject=IKYGVISYENVKQDLLDWRWIYISGRLHKPVLEVIKPRQDMCDLVTENRR...
    Signif=1.00
    Length=85
    Bits=21.5
    Query_start=119
    Subject_end=190
    Query=LKFNLNLRLTVNIDQLEWEVLHVS--LHFWVVEVSTDQT----LSVENGIRRI...
    Positives=46%25
    Expect=9.5,
    Identity=26%25
    Query_end=203
    Orientation=plus
    Score=61
    Subject_start=98
    Alignment=+K+ +     V  D L+W  +++S  LH  V+EV   +     L  EN ...
  }
}
=