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pepinfo |
It can plot and display the following properties:
The data are also written out to a data file.
% pepinfo Plots simple amino acid properties in parallel Input sequence: sw:opsd_human Graph type [x11]: Output file [pepinfo.out]:
Click here to see the histogram
Click here to see the hydrophobicity plots
Mandatory qualifiers: [-inseq] sequence Sequence USA -graph xygraph Graph type [-outfile] outfile Output file name Optional qualifiers: -hwindow integer Window size for hydropathy averaging -aaproperties string User defined amino acid properties -aahydropathy string User defined hydropathy data Advanced qualifiers: -[no]generalplot boolean plot histogram of general properties -[no]hydropathyplot boolean plot graphs of hydropathy General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-inseq] (Parameter 1) |
Sequence USA | Readable sequence | Required |
-graph | Graph type | EMBOSS has a list of known devices, including postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows, x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm, png | EMBOSS_GRAPHICS value, or x11 |
[-outfile] (Parameter 2) |
Output file name | Output file | pepinfo.out |
Optional qualifiers | Allowed values | Default | |
-hwindow | Window size for hydropathy averaging | Integer 1 or more | 9 |
-aaproperties | User defined amino acid properties | Any string is accepted | Eaa_properties.dat |
-aahydropathy | User defined hydropathy data | Any string is accepted | Eaa_hydropathy.dat |
Advanced qualifiers | Allowed values | Default | |
-[no]generalplot | plot histogram of general properties | Yes/No | Yes |
-[no]hydropathyplot | plot graphs of hydropathy | Yes/No | Yes |
The output file contains the coordinates from the graphs.
For the first set of graphs, 9 sets of true/false values are written out. For the second set of graphs, 3 sets of hydrophobicity values are written.
Printing out Tiny residues in OPSD_HUMAN from position 1 to 348 Position Residue Result 1 M 0 2 N 0 3 G 1 4 T 1 5 E 0 6 G 1 7 P 0 8 N 0 9 F 0 10 Y 0 .................... 341 E 0 342 T 1 343 S 1 344 Q 0 345 V 0 346 A 1 347 P 0 348 A 1 Printing out Small residues in OPSD_HUMAN from position 1 to 348 Position Residue Result 1 M 0 2 N 1 3 G 1 4 T 1 5 E 0 6 G 1 7 P 1 8 N 1 9 F 0 10 Y 0
The hydropathy data of the residues are read from the EMBOSS data file 'Eaa_hydropathy.dat'. This file can be copied into your current directory and inspected ot altered by using the application 'embossdata -fetch'. Another file can be specified using the qualifier '-aahydropathy'.
EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by EMBOSS environment variable EMBOSS_DATA.
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 |
---|---|
backtranseq | Back translate a protein sequence |
charge | Protein charge plot |
checktrans | Reports STOP codons and ORF statistics of a protein sequence |
compseq | Counts the 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 |
mwfilter | Filter noisy molwts from mass spec output |
octanol | Displays protein hydropathy |
pepstats | Protein statistics |
pepwindow | Displays protein hydropathy |
pepwindowall | Displays protein hydropathy of a set of sequences |