seqnr - Removes redundancy from DHF files.

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

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).

       seqnr - Removes redundancy from DHF files.

Inputsection-dhfinpathdirlist
           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: ./

       -dosingtoggle
           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

       -singletsdirdirectory
           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: ./

       -dosetstoggle
           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

       -insetsdirdirectory
           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: ./

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

   Requiredsection-modelist
           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

       -threshfloat
           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

       -threshlowfloat
           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

       -threshupfloat
           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

   Additionalsection-gapopenfloat
           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

       -gapextendfloat
           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

   Outputsection-dhfoutdiroutdir
           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: ./

       -doredtoggle
           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

       -redoutdiroutdir
           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: ./

       -logfileoutfile
           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

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

seqnr-dhfinpathdirlist-dosingtoggle-singletsdirdirectory-dosetstoggle-insetsdirdirectory
             [-matrixmatrixf] -modelist-threshfloat-threshlowfloat-threshupfloat [-gapopenfloat]
             [-gapextendfloat] -dhfoutdiroutdir-doredtoggle-redoutdiroutdir-logfileoutfileseqnr-help