pepinfo

 

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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 

Plot amino acid properties of a protein sequence in parallel.
Version: EMBOSS:6.6.0.0

   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,
                                  tek, tekt, none, data, xterm, png, gif, pdf,
                                  svg)
  [-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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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 and exit. 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
   -version            boolean    Report version number and exit

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-sequence]
(Parameter 1)		 sequence Protein sequence filename and optional format, or reference (input USA) Readable sequence Required
-graph xygraph Graph type EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, pdf, svg EMBOSS_GRAPHICS value, or x11
[-outfile]
(Parameter 2)		 outfile Output file name Output file <*>.pepinfo
Additional (Optional) qualifiers
-aaproperties datafile Amino acid chemical classes data file Data file Eaa_properties.dat
-aahydropathy datafile Amino acid hydropathy values data file Data file Eaa_hydropathy.dat
-hwindow integer Window size for hydropathy averaging Integer 1 or more 9
Advanced (Unprompted) qualifiers
-[no]generalplot boolean Plot histogram of general properties Boolean value Yes/No Yes
-[no]hydropathyplot boolean Plot graphs of hydropathy Boolean value Yes/No Yes
Associated qualifiers
"-sequence" associated sequence qualifiers
-sbegin1
-sbegin_sequence		 integer Start of the sequence to be used Any integer value 0
-send1
-send_sequence		 integer End of the sequence to be used Any integer value 0
-sreverse1
-sreverse_sequence		 boolean Reverse (if DNA) Boolean value Yes/No N
-sask1
-sask_sequence		 boolean Ask for begin/end/reverse Boolean value Yes/No N
-snucleotide1
-snucleotide_sequence		 boolean Sequence is nucleotide Boolean value Yes/No N
-sprotein1
-sprotein_sequence		 boolean Sequence is protein Boolean value Yes/No N
-slower1
-slower_sequence		 boolean Make lower case Boolean value Yes/No N
-supper1
-supper_sequence		 boolean Make upper case Boolean value Yes/No N
-scircular1
-scircular_sequence		 boolean Sequence is circular Boolean value Yes/No N
-squick1
-squick_sequence		 boolean Read id and sequence only Boolean value Yes/No N
-sformat1
-sformat_sequence		 string Input sequence format Any string  
-iquery1
-iquery_sequence		 string Input query fields or ID list Any string  
-ioffset1
-ioffset_sequence		 integer Input start position offset Any integer value 0
-sdbname1
-sdbname_sequence		 string Database name Any string  
-sid1
-sid_sequence		 string Entryname Any string  
-ufo1
-ufo_sequence		 string UFO features Any string  
-fformat1
-fformat_sequence		 string Features format Any string  
-fopenfile1
-fopenfile_sequence		 string Features file name Any string  
"-graph" associated xygraph qualifiers
-gprompt boolean Graph prompting Boolean value Yes/No N
-gdesc string Graph description Any string  
-gtitle string Graph title Any string  
-gsubtitle string Graph subtitle Any string  
-gxtitle string Graph x axis title Any string  
-gytitle string Graph y axis title Any string  
-goutfile string Output file for non interactive displays Any string  
-gdirectory string Output directory Any string  
"-outfile" associated outfile qualifiers
-odirectory2
-odirectory_outfile		 string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

Input file format

pepinfo reads a single protein sequence.

The input is a standard EMBOSS sequence query (also known as a 'USA').

Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl

Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.

The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.

See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.

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   13-JUN-2012, entry version 145.
DE   RecName: Full=Rhodopsin;
DE   AltName: Full=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; DOI=10.1073/pnas.81.15.4851;
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;
RX   PubMed=17974005; DOI=10.1186/1471-2164-8-399;
RA   Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U.,
RA   Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H.,
RA   Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K.,
RA   Ottenwaelder B., Poustka A., Wiemann S., Schupp I.;
RT   "The full-ORF clone resource of the German cDNA consortium.";
RL   BMC Genomics 8:399-399(2007).
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.";


  [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; dbSNP:rs28933993).
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; dbSNP:rs29001653).
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; dbSNP:rs29001566).
FT                                /FTId=VAR_004836.
FT   VARIANT     347    347       P -> S (in RP4; dbSNP:rs29001637).
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

The output is to the specified graphics device.

The results can be output in one of several formats by using the command-line qualifier -graph xxx, where 'xxx' is replaced by the name of the required device. Support depends on the availability of third-party software packages.

The device names that output to a file are: ps (postscript), cps (colourps), png, gif, pdf, svg, hpgl, hp7470, hp7580, das, data.

The other available device names are: meta, x11 (xwindows), tek (tek4107t), tekt (tektronix), xterm, text.

Output can be turned off by specifying none (null).

See: http://emboss.sf.net/docs/themes/GraphicsDevices.html for further information on supported devices.

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

[pepinfo results]

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:

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
abiview Display the trace in an ABI sequencer file
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
cirdna Draw circular map of DNA constructs
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
hmoment Calculate and plot hydrophobic moment for protein sequence(s)
iep Calculate the isoelectric point of proteins
lindna Draw linear maps of DNA constructs
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
oddcomp Identify proteins with specified sequence word composition
pepdigest Report on protein proteolytic enzyme or reagent cleavage sites
pepnet Draw a helical net for a protein sequence
pepstats Calculate statistics of protein properties
pepwheel Draw a helical wheel diagram for a protein sequence
pepwindow Draw a hydropathy plot for a protein sequence
pepwindowall Draw Kyte-Doolittle hydropathy plot for a protein alignment
plotorf Plot potential open reading frames in a nucleotide sequence
prettyplot Draw a sequence alignment with pretty formatting
prettyseq Write a nucleotide sequence and its translation to file
remap Display restriction enzyme binding sites in a nucleotide sequence
showfeat Display features of a sequence in pretty format
showpep Display protein sequences with features in pretty format
sixpack Display a DNA sequence with 6-frame translation and ORFs
wordcount Count and extract unique words in molecular sequence(s)

Author(s)

Mark Faller formerly at:
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

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