EMBOSS: pepstats

| ## EMBOSS: pepstats

# Program pepstats

## Function

Protein statistics

## Description

pepstats outputs a report of simple protein sequence information including:

- molecular weight
- number of residues
- average residue weight
- charge
- isoelectric point
- for each type of amino acid: number, molar percent, DayhoffStat
- for each physico-chemical class of amino acid: number, molar percent

DayhoffStat is the amino acid's Dayhoff statistic divided by the molar percent. The Dayhoff statistic is the amino acid's relative occurence per 1000 aa normalised to 100 by rls@ebi.ac.uk (original work from 1993)

## Usage

Here is a sample session with pepstats.

    % pepstats
    Protein statistics
    Input sequence: sw:laci_ecoli
    Output file [laci_ecoli.pepstats]:

## Command line arguments

       Mandatory qualifiers:
      [-sequencea]         sequence   Sequence USA
       -outfile            outfile    Output file name

       Optional qualifiers: (none)
       Advanced qualifiers:
       -[no]termini        bool       Include charge at N and C terminus
       -aadata             string     Molecular weight data for amino acids

       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequencea] (Parameter 1) | Sequence USA | Readable sequence | Required
-outfile | Output file name | Output file | <sequence>.pepstats
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
-[no]termini | Include charge at N and C terminus | Yes/No | Yes
-aadata | Molecular weight data for amino acids | Any string is accepted | Eamino.dat

## Input file format

Normal protein sequence USA.

## Output file format

Here is the output from the example run:

    PEPSTATS of LACI_ECOLI from 1 to 360

    Molecular weight = 38563.98             Residues = 360
    Average Residue Weight  = 107.122       Charge   = 1.5
    Isoelectric Point = 6.8820

    Residue         Number          Mole%           DayhoffStat
    A = Ala         44              12.222          1.421
    B = Asx         0               0.000           0.000
    C = Cys         3               0.833           0.287
    D = Asp         17              4.722           0.859
    E = Glu         15              4.167           0.694
    F = Phe         4               1.111           0.309
    G = Gly         22              6.111           0.728
    H = His         7               1.944           0.972
    I = Ile         18              5.000           1.111
    K = Lys         11              3.056           0.463
    L = Leu         40              11.111          1.502
    M = Met         10              2.778           1.634
    N = Asn         12              3.333           0.775
    P = Pro         14              3.889           0.748
    Q = Gln         28              7.778           1.994
    R = Arg         19              5.278           1.077
    S = Ser         33              9.167           1.310
    T = Thr         19              5.278           0.865
    V = Val         34              9.444           1.431
    W = Trp         2               0.556           0.427
    X = Xxx         0               0.000           0.000
    Y = Tyr         8               2.222           0.654
    Z = Glx         0               0.000           0.000

    Property        Residues                Number          Mole%
    Tiny            (A+C+G+S+T)             121             33.611
    Small           (A+B+C+D+G+N+P+S+T+V)   198             55.000
    Aliphatic       (I+L+V)                 92              25.556
    Aromatic        (F+H+W+Y)               21               5.833
    Non-polar       (A+C+F+G+I+L+M+P+V+W+Y) 199             55.278
    Polar           (D+E+H+K+N+Q+R+S+T+Z)   161             44.722
    Charged         (B+D+E+H+K+R+Z)         69              19.167
    Basic           (H+K+R)                 37              10.278
    Acidic          (B+D+E+Z)               32               8.889

## Data files

The Dayhoff statistic is read from the EMBOSS data file 'Edayhoff.freq'. You can inspect and modify this file by copying it into your current directory with the command: 'embossdata -fetch'.

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:

- . (your current directory)
- .embossdata (under your current directory)
- ~/ (your home directory)
- ~/.embossdata

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with a status of 0.

## Known bugs

None.

## See also

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
mwfilter | Filter noisy molwts from mass spec output
octanol | Displays protein hydropathy
pepinfo | Plots simple amino acid properties in parallel
pepwindow | Displays protein hydropathy
pepwindowall | Displays protein hydropathy of a set of sequences

## Author(s)

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

## History

Written (1999) - Alan Bleasby

## Target users

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

## Comments