
                                  sigscan 



Function

   Generates a DHF file (domain hits file) of hits (sequences) from
   scanning a signature against a sequence database

Description

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Algorithm

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Usage

Command line arguments

   Standard (Mandatory) qualifiers:
  [-siginfile]         infile     This option specifies the name of the
                                  signature file (input). A 'signature file'
                                  contains a sparse sequence signature
                                  suitable for use with the SIGSCAN program.
                                  The files are generated by using SIGGEN.
  [-dbsequence]        seqall     This option specifies the name of the
                                  database to search.
   -sub                matrixf    This option specifies the residue
                                  substitution matrix.
   -gapo               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 EDNAMAT matrix
                                  for nucleotide sequences.
   -gape               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. An exception is where
                                  one or both sequences are single reads with
                                  possible sequencing errors in which case you
                                  would expect many single base gaps. You can
                                  get this result by setting the gap open
                                  penalty to zero (or very low) and using the
                                  gap extension penalty to control gap
                                  scoring.
   -nterm              menu       This option specifies the N-terminal
                                  matching option. This determines how the
                                  first signature position is aligned to a
                                  sequence from the database.
   -nhits              integer    This option specifies the maximum number of
                                  hits to output.
  [-hitsfile]          outfile    This option specifies the name of the DHF
                                  file (domain hits file) (output). A 'domain
                                  hits file' contains database hits
                                  (sequences) with domain classification
                                  information, in the DHF format (FASTA-like).
                                  The hits are relatives to a SCOP or CATH
                                  family (or other node in the structural
                                  hierarchies) and are found from a search of
                                  a sequence database, in this case, by using
                                  SIGSCAN. Files containing hits retrieved by
                                  PSIBLAST are generated by using SEQSEARCH or
                                  various types of HMM and profile by using
                                  LIBSCAN.
  [-alignfile]         outfile    This option specifies the name of the DAF
                                  (domain alignment file) (output). A 'domain
                                  alignment file' contains a sequence
                                  alignment of domains belonging to the same
                                  SCOP or CATH family (or other node in the
                                  structural hierarchies). The file is in DAF
                                  format (CLUSTAL-like) and is annotated with
                                  domain family classification information.
                                  The files generated by using SIGSCAN will
                                  contain a signature-sequence alignment of
                                  domain sequences returned by scanning a
                                  signature (for a family of domains) against
                                  a sequence database.

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-dbsequence" associated qualifiers
   -sbegin2            integer    Start of each sequence to be used
   -send2              integer    End of each sequence to be used
   -sreverse2          boolean    Reverse (if DNA)
   -sask2              boolean    Ask for begin/end/reverse
   -snucleotide2       boolean    Sequence is nucleotide
   -sprotein2          boolean    Sequence is protein
   -slower2            boolean    Make lower case
   -supper2            boolean    Make upper case
   -sformat2           string     Input sequence format
   -sdbname2           string     Database name
   -sid2               string     Entryname
   -ufo2               string     UFO features
   -fformat2           string     Features format
   -fopenfile2         string     Features file name

   "-hitsfile" associated qualifiers
   -odirectory3        string     Output directory

   "-alignfile" associated qualifiers
   -odirectory4        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-siginfile]
   (Parameter 1) This option specifies the name of the signature file
   (input). A 'signature file' contains a sparse sequence signature
   suitable for use with the SIGSCAN program. The files are generated by
   using SIGGEN. Input file Required
   [-dbsequence]
   (Parameter 2) This option specifies the name of the database to
   search. Readable sequence(s) Required
   -sub This option specifies the residue substitution matrix. Comparison
   matrix file in EMBOSS data path EBLOSUM62
   -gapo 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 EDNAMAT matrix for nucleotide sequences. Floating
   point number from 1.0 to 100.0 10.0 for any sequence
   -gape 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. An
   exception is where one or both sequences are single reads with
   possible sequencing errors in which case you would expect many single
   base gaps. You can get this result by setting the gap open penalty to
   zero (or very low) and using the gap extension penalty to control gap
   scoring. Floating point number from 0.0 to 10.0 0.5 for any sequence
   -nterm This option specifies the N-terminal matching option. This
   determines how the first signature position is aligned to a sequence
   from the database.
   1 (Align anywhere and allow only complete signature-sequence fit)
   2 (Align anywhere and allow partial signature-sequence fit)
   3 (Use empirical gaps only)
   1
   -nhits This option specifies the maximum number of hits to output. Any
   integer value 100
   [-hitsfile]
   (Parameter 3) This option specifies the name of the DHF file (domain
   hits file) (output). A 'domain hits file' contains database hits
   (sequences) with domain classification information, in the DHF format
   (FASTA-like). The hits are relatives to a SCOP or CATH family (or
   other node in the structural hierarchies) and are found from a search
   of a sequence database, in this case, by using SIGSCAN. Files
   containing hits retrieved by PSIBLAST are generated by using SEQSEARCH
   or various types of HMM and profile by using LIBSCAN. Output file
   SIGSCAN.dhf
   [-alignfile]
   (Parameter 4) This option specifies the name of the DAF (domain
   alignment file) (output). A 'domain alignment file' contains a
   sequence alignment of domains belonging to the same SCOP or CATH
   family (or other node in the structural hierarchies). The file is in
   DAF format (CLUSTAL-like) and is annotated with domain family
   classification information. The files generated by using SIGSCAN will
   contain a signature-sequence alignment of domain sequences returned by
   scanning a signature (for a family of domains) against a sequence
   database. Output file SIGSCAN.aln
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

Input file format

   sigscan reads any normal sequence USAs.

Output file format

   sigscan outputs a graph to the specified graphics device. outputs a
   report format file. The default format is ...

Data files

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Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name Description
   contactcount Counts specific versus non-specific contacts in a
   directory of cleaned protein chain contact files
   contacts Reads CCF files (clean coordinate files) and writes CON files
   (contact files) of intra-chain residue-residue contact data
   domainalign Generates DAF files (domain alignment files) of
   structure-based sequence alignments for nodes in a DCF file (domain
   classification file)
   domainrep Reorder DCF file (domain classification file) so that the
   representative structure of each user-specified node is given first
   domainreso Removes low resolution domains from a DCF file (domain
   classification file)
   interface Reads CCF files (clean coordinate files) and writes CON
   files (contact files) of inter-chain residue-residue contact data
   libgen Generates various types of discriminating elements for each
   alignment in a directory
   psiphi Calculates phi and psi torsion angles from cleaned EMBOSS-style
   protein co-ordinate file
   rocon Reads a DHF file (domain hits file) of hits (sequences of
   unknown structural classification) and a DHF file of validation
   sequences (known classification) and writes a 'hits file' for the
   hits, which are classified and rank-ordered on the basis of score
   rocplot Provides interpretation and graphical display of the
   performance of discriminating elements (e.g. profiles for protein
   families). rocplot reads file(s) of hits from discriminator-database
   search(es), performs ROC analysis on the hits, and writes graphs
   illustrating the diagnostic performance of the discriminating elements
   seqalign Reads a DAF file (domain alignment file) and a DHF file
   (domain hits file) and writes a DAF file extended with the hits
   seqfraggle Removes fragments from DHF files (domain hits files) or
   other files of sequences
   seqsearch Generate database hits (sequences) for nodes in a DCF file
   (domain classification file) by using PSI-BLAST
   seqsort Reads DHF files (domain hits files) of database hits
   (sequences) and removes hits of ambiguous classification
   seqwords Generates DHF files (domain hits files) of database hits
   (sequences) for nodes in a DCF file (domain classification file) by
   keyword search of UniProt
   siggen Generates a sparse protein signature from an alignment and
   residue contact data

Author(s)

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History

   Written (date) - author.

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
