## EMBOSS: seqnr

# Program seqnr

## Function

Converts redundant database results to a non-redundant set of hits

## Description

This is part of Jon Ison's protein structure analysis package.

This package is still being developed.

Please ignore this program until further details can be documented.

All further queries should go to Jon Ison. (Jon Ison)

## Usage

Here is a sample session with seqnr:

    % seqnr

## Command line arguments

       Mandatory qualifiers:
      [-path]              string     Directory of redundant database search
                                      results
      [-extn]              string     File extension of redundant database search
                                      results files
      [-outpath]           string     Directory for proccessed results
      [-outextn]           string     File extension for proccessed results files
      [-datafile]          matrixf    Residue substitution matrix
      [-gapopen]           float      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.
      [-gapextend]         float      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.
      [-thresh]            float      The % sequence identity redundancy threshold

       Optional qualifiers: (none)
       Advanced qualifiers: (none)
       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-path] (Parameter 1) | Directory of redundant database search results | Any string is accepted | ./
[-extn] (Parameter 2) | File extension of redundant database search results files | Any string is accepted | .psiblasts
[-outpath] (Parameter 3) | Directory for proccessed results | Any string is accepted | ./
[-outextn] (Parameter 4) | File extension for proccessed results files | Any string is accepted | .clean
[-datafile] (Parameter 5) | Residue substitution matrix | Comparison matrix file in EMBOSS data path | EBLOSUM62
[-gapopen] (Parameter 6) | 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. | Floating point number from 1.0 to 100.0 | 10.0 for any sequence

[-gapextend]
(Parameter 7)

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

[-thresh] (Parameter 8) | The % sequence identity redundancy threshold | Any integer value | 95.0
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

## Output file format

## Data files

## 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
--- | ---
cutgextract | Extract data from CUTG
domainer | Build domain coordinate files
nrscope | Converts redundant EMBL-format SCOP file to non-redundant one
pdbtosp | Convert raw swissprot:pdb equivalence file to embl-like format
printsextract | Extract data from PRINTS
prosextract | Builds the PROSITE motif database for patmatmotifs to search
rebaseextract | Extract data from REBASE
scope | Convert raw scop classification file to embl-like format
scopparse | Reads raw-, and writes EMBL-like, scop classification files
tfextract | Extract data from TRANSFAC

## Author(s)

This application was written by Jon Ison (jison@hgmp.mrc.ac.uk)

## History

Written (date) - author.

## Target users

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

## Comments