DIFFSEQ(1e) | EMBOSS Manual for Debian | DIFFSEQ(1e) |
NAME¶
diffseq - Compare and report features of two similar sequencesSYNOPSIS¶
diffseq -asequence sequence
-bsequence sequence
-wordsize integer
[-globaldifferences boolean]
-outfile report
-aoutfeat featout
-boutfeat featout
diffseq -help
DESCRIPTION¶
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).OPTIONS¶
Input section¶
-asequence sequence -bsequence sequenceRequired section¶
-wordsize integerThe 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
Additional section¶
-globaldifferences booleanNormally 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
Output section¶
-outfile report -aoutfeat featoutFile for output of first sequence's features Default
value: $(asequence.name).diffgff
-boutfeat featout
File for output of second sequence's features Default
value: $(bsequence.name).diffgff
BUGS¶
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).SEE ALSO¶
diffseq is fully documented via the tfm(1) system.AUTHOR¶
Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>Wrote the script used to autogenerate this manual
page.
COPYRIGHT¶
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.05/11/2012 | EMBOSS 6.4.0 |