SEQNR(1e)						     EMBOSS Manual for Debian							 SEQNR(1e)

NAME

       seqnr - Removes redundancy from DHF files.

SYNOPSIS

       seqnr -dhfinpath dirlist -dosing toggle -singletsdir directory -dosets toggle -insetsdir directory [-matrix matrixf] -mode list
	     -thresh float -threshlow float -threshup float [-gapopen float] [-gapextend float] -dhfoutdir outdir -dored toggle -redoutdir outdir
	     -logfile outfile

       seqnr -help

DESCRIPTION

       seqnr is a command line program from EMBOSS ("the European Molecular Biology Open Software Suite"). It is part of the "Utils:Database
       creation" command group(s).

OPTIONS

   Input section
       -dhfinpath dirlist
	   This option specifies the location of DHF files (domain hits files) (input). A 'domain hits file' contains database hits (sequences)
	   with domain classification information, in the DHF format (FASTA or EMBL-like). The hits are relatives to a SCOP or CATH family and are
	   found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH. Default
	   value: ./

       -dosing toggle
	   This option specifies whether to use singlet sequences (e.g. DHF files) to filter input. Optionally, up to two further directories of
	   sequences may be read: these are considered in the redundancy calculation but never appear in the output files. Default value: Y

       -singletsdir directory
	   This option specifies the location of singlet filter sequences (e.g. DHF files) (input). A 'domain hits file' contains database hits
	   (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). The hits are relatives to a SCOP or CATH
	   family and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using
	   SEQSEARCH. Default value: ./

       -dosets toggle
	   This option specifies whether to use sets of sequences (e.g. DHF files) to filter input. Optionally, up to two further directories of
	   sequences may be read: these are considered in the redundancy calculation but never appear in the output files. Default value: Y

       -insetsdir directory
	   This option specifies location of sets of filter sequences (e.g. DAF files) (input). A 'domain alignment file' contains a sequence
	   alignment of domains belonging to the same SCOP or CATH family. The file is in clustal format annotated with domain family
	   classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of
	   known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN. Default value:
	   ./

       -matrix matrixf
	   This option specifies the residue substitution matrix that is used for sequence comparison. Default value: EBLOSUM62

   Required section
       -mode list
	   This option specifies whether to remove redundancy at a single threshold % sequence similarity or remove redundancy outside a range of
	   acceptable threshold % similarity. All permutations of pair-wise sequence alignments are calculated for each set of input sequences in
	   turn using the EMBOSS implementation of the Needleman and Wunsch global alignment algorithm. Redundant sequences are removed in one of
	   two modes as follows: (i) If a pair of proteins achieve greater than a threshold percentage sequence similarity (specified by the user)
	   the shortest sequence is discarded. (ii) If a pair of proteins have a percentage sequence similarity that lies outside an acceptable
	   range (specified by the user) the shortest sequence is discarded. Default value: 1

       -thresh float
	   This option specifies the % sequence identity redundancy threshold. The % sequence identity redundancy threshold determines the
	   redundancy calculation. If a pair of proteins achieve greater than this threshold the shortest sequence is discarded. Default value:
	   95.0

       -threshlow float
	   This option specifies the % sequence identity redundancy threshold (lower limit). The % sequence identity redundancy threshold
	   determines the redundancy calculation. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable
	   range the shortest sequence is discarded. Default value: 30.0

       -threshup float
	   This option specifies the % sequence identity redundancy threshold (upper limit). The % sequence identity redundancy threshold
	   determines the redundancy calculation. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable
	   range the shortest sequence is discarded. Default value: 90.0

   Additional section
       -gapopen float
	   This option specifies the gap insertion penalty. The gap insertion penalty is the score taken away when a gap is created. The best
	   value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences,
	   and the EDNAFULL matrix for nucleotide sequences. Default value: 10

       -gapextend float
	   This option specifies the gap extension penalty. The gap extension, penalty is added to the standard gap penalty for each base or
	   residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the
	   gap extension penalty should be lower than the gap penalty. Default value: 0.5

   Output section
       -dhfoutdir outdir
	   This option specifies the location of DHF files (domain hits files) of non-redundant sequences (output). A 'domain hits file' contains
	   database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). The hits are relatives to a
	   SCOP or CATH family and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by
	   using SEQSEARCH. Default value: ./

       -dored toggle
	   This option specifies whether to retain redundant sequences. If this option is set a DHF file (domain hits file) of redundant sequences
	   is written. Default value: N

       -redoutdir outdir
	   This option specifies the location of DHF files (domain hits files) of redundant sequences (output). A 'domain hits file' contains
	   database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). The hits are relatives to a
	   SCOP or CATH family and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by
	   using SEQSEARCH. Default value: ./

       -logfile outfile
	   This option specifies the name of SEQNR log file (output). The log file contains messages about any errors arising while SEQNR ran.
	   Default value: seqnr.log

BUGS

       Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers
       (http://sourceforge.net/tracker/?group_id=93650&atid=605031).

SEE ALSO

       seqnr is fully documented via the tfm(1) system.

AUTHOR

       Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
	   Wrote the script used to autogenerate this manual page.

COPYRIGHT

       This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as
       EMBOSS itself.

DOMSEARCH 0.1.0++20100721					    08/11/2010								 SEQNR(1e)