EMBOSS: emowse


Program emowse

Function

Protein identification by mass spectrometry

Description

Given a one-per-line file of molecular weights this program will search a protein database for matches with the mass spectrometry data. Eight enzymes/reagents can be specified and an optional whole sequence molecular weight.

Usage

Here is a sample session with emowse:

% emowse

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EDIT HERE
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Command line arguments

   Mandatory qualifiers:
  [-sequences]         seqall     Sequence database USA
  [-infile]            infile     Name of molecular weight data file
   -weight             integer    Whole sequence molwt
   -outfile            outfile    Output file name

   Optional qualifiers: (none)
   Advanced qualifiers:
   -enzyme             list       Enzyme or reagent
   -pcrange            integer    Allowed whole sequence weight variability
   -frequencies        string     Frequencies file
   -tolerance          float      (no help text) float value
   -partials           float      Partials factor


Mandatory qualifiers Allowed values Default
[-sequences]
(Parameter 1)
Sequence database USA Readable sequence(s) Required
[-infile]
(Parameter 2)
Name of molecular weight data file Input file Required
-weight Whole sequence molwt Any integer value 0
-outfile Output file name Output file <sequence>.emowse
Optional qualifiers Allowed values Default
(none)
Advanced qualifiers Allowed values Default
-enzyme Enzyme or reagent
1 (Trypsin)
2 (Lys-C)
3 (Arg-C)
4 (Asp-N)
5 (V8-bicarb)
6 (V8-phosph)
7 (Chymotrypsin)
8 (CNBr)
1
-pcrange Allowed whole sequence weight variability Integer from 0 to 75 25
-frequencies Frequencies file Any string is accepted Efreqs.dat
-tolerance (no help text) float value Number from 0.100 to 1.000 0.1
-partials Partials factor Number from 0.100 to 1.000 0.4

Input file format

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Output file format

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Data files

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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
compseqCounts the composition of dimer/trimer/etc words in a sequence
oddcompFinds protein sequence regions with a biased composition

Author(s)

This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)

History

Written (Sept 2000) - author.

Target users

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

Comments