EMBOSS: pepinfo

| pepinfo

## Function

Plot amino acid properties of a protein sequence in parallel

## Description

pepinfo plots various amino acid properties in parallel for an input protein sequence. The types of plot available are i. Hydrophobicity plots using the method of Kyte & Doolittle, the optimal matching hydrophobicity scale (OHM) of Sweet & Eisenberg, or consensus parameters (Eisenberg et al). ii. Histogram of the presence of residues with the physico-chemical properties: Tiny, Small, Aliphatic, Aromatic, Non-polar, Polar, Charged, Positive, Negative. The data are also written out to an output file.

## Usage

Here is a sample session with pepinfo

    % pepinfo
    Plot amino acid properties of a protein sequence in parallel.
    Input protein sequence: tsw:opsd_human
    Graph type [x11]: cps
    Output file [opsd_human.pepinfo]:

    Created pepinfo.ps

Go to the input files for this example
Go to the output files for this example

## Command line arguments

       Standard (Mandatory) qualifiers:
      [-sequence]          sequence   Protein sequence filename and optional
                                      format, or reference (input USA)
       -graph              xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
                                      (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                      tekt, tek, none, data, xterm, png, gif)
      [-outfile]           outfile    [*.pepinfo] Output file name

       Additional (Optional) qualifiers:
       -aaproperties       datafile   [Eaa_properties.dat] Amino acid chemical
                                      classes data file
       -aahydropathy       datafile   [Eaa_hydropathy.dat] Amino acid hydropathy
                                      values data file
       -hwindow            integer    [9] Window size for hydropathy averaging
                                      (Integer 1 or more)

       Advanced (Unprompted) qualifiers:
       -[no]generalplot    boolean    [Y] Plot histogram of general properties
       -[no]hydropathyplot boolean    [Y] Plot graphs of hydropathy

       Associated qualifiers:

       "-sequence" associated qualifiers
       -sbegin1            integer    Start of the sequence to be used
       -send1              integer    End of the sequence to be used
       -sreverse1          boolean    Reverse (if DNA)
       -sask1              boolean    Ask for begin/end/reverse
       -snucleotide1       boolean    Sequence is nucleotide
       -sprotein1          boolean    Sequence is protein
       -slower1            boolean    Make lower case
       -supper1            boolean    Make upper case
       -sformat1           string     Input sequence format
       -sdbname1           string     Database name
       -sid1               string     Entryname
       -ufo1               string     UFO features
       -fformat1           string     Features format
       -fopenfile1         string     Features file name

       "-graph" associated qualifiers
       -gprompt            boolean    Graph prompting
       -gdesc              string     Graph description
       -gtitle             string     Graph title
       -gsubtitle          string     Graph subtitle
       -gxtitle            string     Graph x axis title
       -gytitle            string     Graph y axis title
       -goutfile           string     Output file for non interactive displays
       -gdirectory         string     Output directory

       "-outfile" associated qualifiers
       -odirectory2        string     Output directory

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to 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
--- | --- | ---
[-sequence] (Parameter 1) | Protein sequence filename and optional format, or reference (input USA) | Readable sequence | Required
-graph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, xterm, png, gif | EMBOSS_GRAPHICS value, or x11
[-outfile] (Parameter 2) | Output file name | Output file | <*>.pepinfo
Additional (Optional) qualifiers | Allowed values | Default
-aaproperties | Amino acid chemical classes data file | Data file | Eaa_properties.dat
-aahydropathy | Amino acid hydropathy values data file | Data file | Eaa_hydropathy.dat
-hwindow | Window size for hydropathy averaging | Integer 1 or more | 9
Advanced (Unprompted) qualifiers | Allowed values | Default
-[no]generalplot | Plot histogram of general properties | Boolean value Yes/No | Yes
-[no]hydropathyplot | Plot graphs of hydropathy | Boolean value Yes/No | Yes

## Input file format

pepinfo reads a protein sequence USA.

### Input files for usage example

'tsw:opsd_human' is a sequence entry in the example protein database 'tsw'

### Database entry: tsw:opsd_human

    ID   OPSD_HUMAN              Reviewed;         348 AA.
    AC   P08100; Q16414; Q2M249;
    DT   01-AUG-1988, integrated into UniProtKB/Swiss-Prot.
    DT   01-AUG-1988, sequence version 1.
    DT   20-MAR-2007, entry version 91.
    DE   Rhodopsin (Opsin-2).
    GN   Name=RHO; Synonyms=OPN2;
    OS   Homo sapiens (Human).
    OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
    OC   Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
    OC   Catarrhini; Hominidae; Homo.
    OX   NCBI_TaxID=9606;
    RN   [1]
    RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    RX   MEDLINE=84272729; PubMed=6589631;
    RA   Nathans J., Hogness D.S.;
    RT   "Isolation and nucleotide sequence of the gene encoding human
    RT   rhodopsin.";
    RL   Proc. Natl. Acad. Sci. U.S.A. 81:4851-4855(1984).
    RN   [2]
    RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    RA   Suwa M., Sato T., Okouchi I., Arita M., Futami K., Matsumoto S.,
    RA   Tsutsumi S., Aburatani H., Asai K., Akiyama Y.;
    RT   "Genome-wide discovery and analysis of human seven transmembrane helix
    RT   receptor genes.";
    RL   Submitted (JUL-2001) to the EMBL/GenBank/DDBJ databases.
    RN   [3]
    RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    RC   TISSUE=Retina;
    RG   The German cDNA consortium;
    RL   Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases.
    RN   [4]
    RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    RX   PubMed=15489334; DOI=10.1101/gr.2596504;
    RG   The MGC Project Team;
    RT   "The status, quality, and expansion of the NIH full-length cDNA
    RT   project: the Mammalian Gene Collection (MGC).";
    RL   Genome Res. 14:2121-2127(2004).
    RN   [5]
    RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-120.
    RX   PubMed=8566799; DOI=10.1016/0378-1119(95)00688-5;
    RA   Bennett J., Beller B., Sun D., Kariko K.;
    RT   "Sequence analysis of the 5.34-kb 5' flanking region of the human
    RT   rhodopsin-encoding gene.";
    RL   Gene 167:317-320(1995).
    RN   [6]
    RP   REVIEW ON RP4 VARIANTS.
    RX   MEDLINE=94004905; PubMed=8401533;
    RA   Al-Maghtheh M., Gregory C., Inglehearn C., Hardcastle A.,
    RA   Bhattacharya S.;

      [Part of this file has been deleted for brevity]

    FT                                /FTId=VAR_004816.
    FT   VARIANT     209    209       V -> M (effect not known).
    FT                                /FTId=VAR_004817.
    FT   VARIANT     211    211       H -> P (in RP4).
    FT                                /FTId=VAR_004818.
    FT   VARIANT     211    211       H -> R (in RP4).
    FT                                /FTId=VAR_004819.
    FT   VARIANT     216    216       M -> K (in RP4).
    FT                                /FTId=VAR_004820.
    FT   VARIANT     220    220       F -> C (in RP4).
    FT                                /FTId=VAR_004821.
    FT   VARIANT     222    222       C -> R (in RP4).
    FT                                /FTId=VAR_004822.
    FT   VARIANT     255    255       Missing (in RP4).
    FT                                /FTId=VAR_004823.
    FT   VARIANT     264    264       Missing (in RP4).
    FT                                /FTId=VAR_004824.
    FT   VARIANT     267    267       P -> L (in RP4).
    FT                                /FTId=VAR_004825.
    FT   VARIANT     267    267       P -> R (in RP4).
    FT                                /FTId=VAR_004826.
    FT   VARIANT     292    292       A -> E (in CSNBAD1).
    FT                                /FTId=VAR_004827.
    FT   VARIANT     296    296       K -> E (in RP4).
    FT                                /FTId=VAR_004828.
    FT   VARIANT     297    297       S -> R (in RP4).
    FT                                /FTId=VAR_004829.
    FT   VARIANT     342    342       T -> M (in RP4).
    FT                                /FTId=VAR_004830.
    FT   VARIANT     345    345       V -> L (in RP4).
    FT                                /FTId=VAR_004831.
    FT   VARIANT     345    345       V -> M (in RP4).
    FT                                /FTId=VAR_004832.
    FT   VARIANT     347    347       P -> A (in RP4).
    FT                                /FTId=VAR_004833.
    FT   VARIANT     347    347       P -> L (in RP4; common variant).
    FT                                /FTId=VAR_004834.
    FT   VARIANT     347    347       P -> Q (in RP4).
    FT                                /FTId=VAR_004835.
    FT   VARIANT     347    347       P -> R (in RP4).
    FT                                /FTId=VAR_004836.
    FT   VARIANT     347    347       P -> S (in RP4).
    FT                                /FTId=VAR_004837.
    SQ   SEQUENCE   348 AA;  38893 MW;  6F4F6FCBA34265B2 CRC64;
         MNGTEGPNFY VPFSNATGVV RSPFEYPQYY LAEPWQFSML AAYMFLLIVL GFPINFLTLY
         VTVQHKKLRT PLNYILLNLA VADLFMVLGG FTSTLYTSLH GYFVFGPTGC NLEGFFATLG
         GEIALWSLVV LAIERYVVVC KPMSNFRFGE NHAIMGVAFT WVMALACAAP PLAGWSRYIP
         EGLQCSCGID YYTLKPEVNN ESFVIYMFVV HFTIPMIIIF FCYGQLVFTV KEAAAQQQES
         ATTQKAEKEV TRMVIIMVIA FLICWVPYAS VAFYIFTHQG SNFGPIFMTI PAFFAKSAAI
         YNPVIYIMMN KQFRNCMLTT ICCGKNPLGD DEASATVSKT ETSQVAPA
    //

## Output file format

Graphs are written to the selected graphics device.

### Output files for usage example

### File: opsd_human.pepinfo

    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
          11       V                               0
          12       P                               0
          13       F                               0
          14       S                               1
          15       N                               0
          16       A                               1
          17       T                               1
          18       G                               1
          19       V                               0
          20       V                               0
          21       R                               0
          22       S                               1
          23       P                               0
          24       F                               0
          25       E                               0
          26       Y                               0
          27       P                               0
          28       Q                               0
          29       Y                               0
          30       Y                               0
          31       L                               0
          32       A                               1
          33       E                               0
          34       P                               0
          35       W                               0
          36       Q                               0
          37       F                               0
          38       S                               1
          39       M                               0
          40       L                               0
          41       A                               1
          42       A                               1
          43       Y                               0
          44       M                               0
          45       F                               0
          46       L                               0
          47       L                               0

      [Part of this file has been deleted for brevity]

      301       Y                           0.500
      302       N                           0.549
      303       P                           0.633
      304       V                           0.636
      305       I                           0.553
      306       Y                           0.438
      307       I                           0.358
      308       M                           0.250
      309       M                           0.262
      310       N                          -0.172
      311       K                          -0.288
      312       Q                          -0.409
      313       F                          -0.409
      314       R                          -0.362
      315       N                          -0.281
      316       C                          -0.120
      317       M                           0.128
      318       L                           0.028
      319       T                           0.341
      320       T                           0.481
      321       I                           0.282
      322       C                           0.124
      323       C                           0.020
      324       G                           0.143
      325       K                           0.202
      326       N                          -0.051
      327       P                          -0.183
      328       L                          -0.298
      329       G                          -0.282
      330       D                          -0.136
      331       D                           0.020
      332       E                           0.001
      333       A                           0.003
      334       S                          -0.070
      335       A                          -0.137
      336       T                          -0.042
      337       V                          -0.042
      338       S                          -0.117
      339       K                          -0.117
      340       T                          -0.280
      341       E                          -0.154
      342       T                          -0.206
      343       S                          -0.172
      344       Q                           0.063
      345       V                           0.000
      346       A                           0.000
      347       P                           0.000
      348       A                           0.000

### Graphics File: pepinfo.ps

The output file 'pepinfo.out' 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.

## Data files

The physico-chemical properties of the residues are read from the EMBOSS data file 'Eaa_properties.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 '-aaproperties'.

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:

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

## Notes

For calculating the hydrophobicity plots, hdrophobicity is calculated in windows of a specified size over the sequence.

The optimal matching hydrophobicity scale (OHM) scale is based on the likelihood of a given amino acid to be replaced by another hydrophobic or "buried" amino acid.

## References

1. Kyte J, Doolittle RF A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982 May 5;157(1):105-132
2. Sweet RM, Eisenberg D Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure. J Mol Biol 1983 Dec 25;171(4):479-488
3. Eisenberg D, Weiss RM, Terwilliger TC. The helical hydrophobic moment: a measure of the amphiphilicity of a helix. Nature 1982 Sep 23;299(5881):371-4

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with a status of 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
backtranambig | Back-translate a protein sequence to ambiguous nucleotide sequence
backtranseq | Back-translate a protein sequence to a nucleotide sequence
charge | Draw a protein charge plot
checktrans | Reports STOP codons and ORF statistics of a protein
compseq | Calculate the composition of unique words in sequences
emowse | Search protein sequences by digest fragment molecular weight
freak | Generate residue/base frequency table or plot
iep | Calculate the isoelectric point of proteins
mwcontam | Find weights common to multiple molecular weights files
mwfilter | Filter noisy data from molecular weights file
octanol | Draw a White-Wimley protein hydropathy plot
pepstats | Calculates statistics of protein properties
pepwindow | Draw a Kyte-Doolittle hydropathy plot for a protein sequence
pepwindowall | Draw Kyte-Doolittle hydropathy plot for a protein alignment
wordcount | Count and extract unique words in DNA sequence(s)

## Author(s)

Mark Faller (current e-mail address unknown)
while he was with:
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

## History

Written (1999) - Mark Faller

## Target users

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

## Comments

None