seqstat(1)							  Biosquid Manual							seqstat(1)

NAME

       seqstat - show statistics and format for a sequence file

SYNOPSIS

       seqstat [options] seqfile

DESCRIPTION

       seqstat reads a sequence file seqfile and shows a number of simple statistics about it.

       The  printed  statistics  include  the  name  of  the  format, the residue type of the first sequence (protein, RNA, or DNA), the number of
       sequences, the total number of residues, and the average and range of the sequence lengths.

OPTIONS

       -a     Show additional verbose information: a table with one line per sequence showing name, length, and description line.  These lines are
	      prefixed with a * character to enable easily grep'ing them out and sorting them.

       -h     Print brief help; includes version number and summary of all options, including expert options.

       -B     (Babelfish).  Autodetect	and  read a sequence file format other than the default (FASTA). Almost any common sequence file format is
	      recognized (including Genbank, EMBL, SWISS-PROT, PIR, and GCG unaligned sequence formats, and Stockholm, GCG MSF, and Clustal align-
	      ment formats). See the printed documentation for a complete list of supported formats.

EXPERT OPTIONS

       --informat <s>
	      Specify  that the sequence file is in format <s>, rather than the default FASTA format.  Common examples include Genbank, EMBL, GCG,
	      PIR, Stockholm, Clustal, MSF, or PHYLIP; see the printed documentation for a complete list of accepted format  names.   This  option
	      overrides the default expected format (FASTA) and the -B Babelfish autodetection option.

       --quiet
	      Suppress the verbose header (program name, release number and date, the parameters and options in effect).

SEE ALSO

       afetch(1), alistat(1), compalign(1), compstruct(1), revcomp(1), seqsplit(1), sfetch(1), shuffle(1), sindex(1), sreformat(1), stranslate(1),
       weight(1).

AUTHOR

       Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine Freely distributed under  the  GNU
       General Public License (GPL) See COPYING in the source code distribution for more details, or contact me.

       Sean Eddy
       HHMI/Department of Genetics
       Washington University School of Medicine
       4444 Forest Park Blvd., Box 8510
       St Louis, MO 63108 USA
       Phone: 1-314-362-7666
       FAX  : 1-314-362-2157
       Email: eddy@genetics.wustl.edu

Biosquid 1.9g							   January 2003 							seqstat(1)