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seqnr.1e.gz

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)
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