patmatdb(1) Searches protein sequences with a sequence motif


patmatdb -sequence seqall -motif string -outfile report
patmatdb -help



is a command line program from EMBOSS ("the European Molecular Biology Open Software Suite"). It is part of the "Protein:Motifs" command group(s).


Input section

-sequence seqall

Required section

-motif string

Patterns for patmatdb are based on the format of pattern used in the PROSITE database. For example: '[DE](2)HS{P}X(2)PX(2,4)C' means two Asps or Glus in any order followed by His, Ser, any residue other then Pro, then two of any residue followed by Pro followed by two to four of any residue followed by Cys. The search is case-independent, so 'AAA' matches 'aaa'.

Output section

-outfile report


Bugs can be reported to the Debian Bug Tracking system (, or directly to the EMBOSS developers (


Debian Med Packaging Team <[email protected]>

Wrote the script used to autogenerate this manual page.


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.