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.