PARSEBLAST(1)						      General Commands Manual						     PARSEBLAST(1)

NAME

       parseblast - Filtering High-scoring Segment Pairs (HSPs) from WU/NCBI BLAST.

SYNOPSIS

       parseblast [options] <results.from.blast>

DESCRIPTION

       This manual page documents briefly the parseblast command.

       Different  output  options  are	available, the most important here are those allowing to write HSPs in GFF format (GFFv1, GFFv2 or APLOT).
       Sequences can be included in the GFF records as a comment field. Furthermore, this script can output also the alignments for  each  HSP	in
       ALN, MSF or tabular formats.

       NOTE  - If first line from blast program output (the one containing which flavour has been run, say here BLASTN, BLASTP, BLASTX, TBLASTN or
       TBLASTX), is missing, the program assumes that it contains BLASTN HSP records. So that, ensure that you feed the parseblast script  with  a
       well  formatted	BLAST file. Sometimes there are no spaces between the HSP coords and its sequence, as it sometimes happens in Web-Blast or
       Paracel-Blast outputs. Now those records are processed ok and that HSP is retrieved as well as "standard" ones.

       WARNING - Frame fields from GFF records generated with parseblast contain BLAST frame (".","1","2","3") instead of the GFF standard  values
       (".","0","1","2"). As the frame for reverse strand must be recalculated from the original sequence length, we suggest users to post-process
       the GFF output from this script with a suitable filter that fix the frames (in case that the program that is going to use the  GFF  records
       will  not work with the original BLAST frames). We provide the command-line option "--no-frame" to set frames to "." (meaning that there is
       no frame).

OPTIONS

       parseblast prints output in "HSP" format by default (see below). It takes input from <STDIN> or single/multiple files, and writes its  out-
       put to <STDOUT>, so user can redirect to a file but he also could use the program as a filter within a pipe.  "-N", "-M", "-P", "-G", "-F",
       "-A" and "-X" options (also the long name versions for each one) are mutually exclusive, and their precedence order is shown above.

       GFF OPTIONS:

       -G, --gff
	      Prints output in GFFv1 format.

       -F, --fullgff
	      Prints output in GFFv2 "alignment" format ("target").

       -A, --aplot
	      Prints output in pseudo-GFF APLOT "alignment" format.

       -S, --subject
	      Projecting GFF output by SUBJECT (default by QUERY).

       -Q, --sequence
	      Append query and subject sequences to GFF record.

       -b, --bit-score
	      Set <score> field to Bits (default Alignment Score).

       -i, --identity-score
	      Set <score> field to Identities (default Alignment).

       -s, --full-scores
	      Include all scores for each HSP in each GFF record.

       -u, --no-frame
	      Set all frames to "." (GFF for not available frames).

       -t, --compact-tags
	      Target coords+strand+frame in short form (NO GFFv2!).

       ALIGNMENT OPTIONS:

       -P, --pairwise
	      Prints pairwise alignment for each HSP in TBL format.

       -M, --msf
	      Prints pairwise alignment for each HSP in MSF format.

       -N, --aln
	      Prints pairwise alignment for each HSP in ALN format.

       -W, --show-coords
	      Adds start/end positions to alignment output.

       GENERAL OPTIONS:

       -X, --expanded
	      Expanded output (producing multiline output records).

       -c, --comments
	      Include parameters from blast program as comments.

       -n, --no-comments
	      Do not print "#" lines (raw output without comments).

       -v, --verbose
	      Warnings sent to <STDERR>.

       --version
	      Prints program version and exits.

       -h, --help
	      Shows this help and exits.

OUTPUT FORMATS
:
	"S_" stands for "Subject_Sequence" and "Q_" for "Query_Sequence". <Program> name is taken from input blast file. <Strands> are	calculated
       from  <start> and <end> positions on original blast file. <Frame> is obtained from the blast file if is present else is set to ".". <SCORE>
       is set to Alignment Score by default, you can change it with "-b" and "-i".
	If "-S" or "--subject" options are given, then QUERY fields are referred to SUBJECT and SUBJECT fields are relative to	QUERY  (this  only
       available for GFF output records).
	Dots  ("...")  mean  that record description continues in the following line, but such record is printed as a single line record by parse-
       blast.

       [HSP] <- (This is the DEFAULT OUTPUT FORMAT)
	<Program> <DataBase> : ...
	  ... <IdentityMatches> <Min_Length> <IdentityScore> ...
	  ... <AlignmentScore> <BitScore> <E_Value> <P_Sum> : ...
	  ... <Q_Name> <Q_Start> <Q_End> <Q_Strand> <Q_Frame> : ...
	  ... <S_Name> <S_Start> <S_End> <S_Strand> <S_Frame> : <S_FullDescription>

       [GFF]
	<Q_Name> <Program> hsp <Q_Start> <Q_End> <SCORE> <Q_Strand> <Q_Frame> <S_Name>

       [FULL GFF] <- (GFF showing alignment data)
	<Q_Name> <Program> hsp <Q_Start> <Q_End> <SCORE> <Q_Strand> <Q_Frame> ...
	  ... Target "<S_Name>" <S_Start> <S_End> ...
	  ... E_value <E_Value> Strand <S_Strand> Frame <S_Frame>

       [APLOT] <- (GFF format enhanced for APLOT program)
	<Q_Name>:<S_Name> <Program> hsp <Q_Start>:<S_Start> <Q_End>:<S_End> <SCORE> ...
	  ... <Q_Strand>:<S_Strand> <Q_Frame>:<S_Frame> <BitScore>:<HSP_Number> ...
	  ... # E_value <E_Value>

       [EXPANDED]
	MATCH(<HSP_Number>): <Q_Name> x <S_Name>
	SCORE(<HSP_Number>): <AlignmentScore>
	BITSC(<HSP_Number>): <BitScore>
	EXPEC(<HSP_Number>): <E_Value> Psum(<P_Sum>)
	IDENT(<HSP_Number>): <IdentityMatches>/<Min_Length> : <IdentityScore> %
	T_GAP(<HSP_Number>): <TotalGaps(BothSeqs)>
	FRAME(<HSP_Number>): <Q_Frame>/<S_Frame>
	STRND(<HSP_Number>): <Q_Strand>/<S_Strand>
	MXLEN(<HSP_Number>): <Max_Length>
	QUERY(<HSP_Number>): length <Q_Length> : gaps <Q_TotalGaps> : ...
	  ... <Q_Start> <Q_End> : <Q_Strand> : <Q_Frame> : <Q_FullSequence>
	SBJCT(<HSP_Number>): length <S_Length> : gaps <S_TotalGaps> : ...
	  ... <S_Start> <S_End> : <S_Strand> : <S_Frame> : <S_FullSequence>

SEE ALSO

       ali2gff(1), blat2gff(1), gff2aplot(1), sim2gff(1).

AUTHOR

       parseblast was written by Josep F. Abril <abril@imim.es>.

       This manual page was written by Nelson A. de Oliveira <naoliv@gmail.com>, for the Debian project (but may be used by others).

							  Mon, 21 Mar 2005 21:44:15 -0300					     PARSEBLAST(1)