EMBOSS: alignwrap

Program alignwrap

Function

Aligns a set of sequences to a seed alignment

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 alignwrap: 

% alignwrap

Command line arguments 

   Mandatory qualifiers:
   -inpath             string     Directory containing the seed alignments
                                  (input)
   -extn               string     File extention of seed alignment files
                                  (input)
   -scopfamilies       string     scop families file containing the set of
                                  sequences in EMBL-like format
   -outpath            string     Directory for extended alignments (output)
   -outextn            string     File extention of extended alignment files
                                  (output)

   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
-inpath Directory containing the seed alignments (input) Any string is accepted ./
-extn File extention of seed alignment files (input) Any string is accepted .align
-scopfamilies scop families file containing the set of sequences in EMBL-like format Any string is accepted An empty string is accepted
-outpath Directory for extended alignments (output) Any string is accepted ./tmp/
-outextn File extention of extended alignment files (output) Any string is accepted .extalign
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 nameDescription
est2genomeAlign EST and genomic DNA sequences
needleNeedleman-Wunsch global alignment
stretcherFinds the best global alignment between two sequences

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