|   | mwfilter | 
The last two operations can be done as most peaks are reported in both modified and unmodified forms. Removal of modified peaks aids in database searching for protein identification.
| % mwfilter Filter noisy molwts from mass spec output Molecular weights file: molwts.dat Ppm tolerance [50.0]: Molecular weights output file [molwts.mwfilter]: | 
Go to the input files for this example
Go to the output files for this example
| 
   Standard (Mandatory) qualifiers:
  [-infile]            infile     Molecular weights file
   -tolerance          float      [50.0] Ppm tolerance (Any numeric value)
  [-outfile]           outfile    [*.mwfilter] Molecular weights output file
   Additional (Optional) qualifiers:
   -showdel            boolean    [N] Output deleted mwts
   Advanced (Unprompted) qualifiers:
   -datafile           datafile   [Emwfilter.dat] Molecular weight standards
                                  data file
   Associated qualifiers:
   "-outfile" associated qualifiers
   -odirectory2        string     Output directory
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
 | 
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-infile] (Parameter 1) | Molecular weights file | Input file | Required | 
| -tolerance | Ppm tolerance | Any numeric value | 50.0 | 
| [-outfile] (Parameter 2) | Molecular weights output file | Output file | <*>.mwfilter | 
| Additional (Optional) qualifiers | Allowed values | Default | |
| -showdel | Output deleted mwts | Boolean value Yes/No | No | 
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| -datafile | Molecular weight standards data file | Data file | Emwfilter.dat | 
| 874.364756 927.450380 1045.572 1068.397129 1121.431124 1163.584593 1305.660840 1428.596448 1479.748341 1502.549157 1554.591658 1567.686209 1576.708354 1639.868056 1748.611920 1753.745298 1880.841178 2383.99 | 
The input file is a simple list of the experimental molecular weights.
There should be one weight per line.
Comments in the data file start with a '#' character in the first column.
Blank lines are ignored.
| 874.364756 927.450380 1068.397129 1121.431124 1163.584593 1305.660840 1428.596448 1479.748341 1502.549157 1554.591658 1567.686209 1576.708354 1639.868056 1748.611920 1753.745298 1880.841178 | 
EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.
To see the available EMBOSS data files, run:
% embossdata -showall
To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:
% embossdata -fetch -file Exxx.dat
Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".
The directories are searched in the following order:
| Program name | Description | 
|---|---|
| backtranambig | Back translate a protein sequence to ambiguous codons | 
| backtranseq | Back translate a protein sequence | 
| charge | Protein charge plot | 
| checktrans | Reports STOP codons and ORF statistics of a protein | 
| compseq | Count composition of dimer/trimer/etc words in a sequence | 
| emowse | Protein identification by mass spectrometry | 
| freak | Residue/base frequency table or plot | 
| iep | Calculates the isoelectric point of a protein | 
| mwcontam | Shows molwts that match across a set of files | 
| octanol | Displays protein hydropathy | 
| pepinfo | Plots simple amino acid properties in parallel | 
| pepstats | Protein statistics | 
| pepwindow | Displays protein hydropathy | 
| pepwindowall | Displays protein hydropathy of a set of sequences |