diffseq - Compare and report features of two similar sequences

DebianMedPackagingTeam <debian-med-packaging@lists.alioth.debian.org>
           Wrote the script used to autogenerate this manual page.

       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).

       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.

EMBOSS 6.4.0                                       05/11/2012                                        DIFFSEQ(1e)

diffseq is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It
       is part of the "Alignment:Differences" command group(s).

       diffseq - Compare and report features of two similar sequences

Inputsection-asequencesequence-bsequencesequenceRequiredsection-wordsizeinteger
           The similar regions between the two sequences are found by creating a hash table of 'wordsize'd
           subsequences. 10 is a reasonable default. Making this value larger (20?) may speed up the program
           slightly, but will mean that any two differences within 'wordsize' of each other will be grouped as a
           single region of difference. This value may be made smaller (4?) to improve the resolution of nearby
           differences, but the program will go much slower. Default value: 10

   Additionalsection-globaldifferencesboolean
           Normally this program will find regions of identity that are the length of the specified word-size or
           greater and will then report the regions of difference between these matching regions. This works
           well and is what most people want if they are working with long overlapping nucleic acid sequences.
           You are usually not interested in the non-overlapping ends of these sequences. If you have protein
           sequences or short RNA sequences however, you will be interested in differences at the very ends . It
           this option is set to be true then the differences at the ends will also be reported. Default value:
           N

   Outputsection-outfilereport-aoutfeatfeatout
           File for output of first sequence's features Default value: $(asequence.name).diffgff

       -boutfeatfeatout
           File for output of second sequence's features Default value: $(bsequence.name).diffgff

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

diffseq-asequencesequence-bsequencesequence-wordsizeinteger [-globaldifferencesboolean]
               -outfilereport-aoutfeatfeatout-boutfeatfeatoutdiffseq-help