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pepinfo |
Function
Plots simple amino acid properties in parallelDescription
pepinfo detects and displays various useful metrics about a protein sequence.It can plot and display the following properties:
- plots of hydrophobicity (using the method of Kyte & Doolittle), of OHM (Sweet & Eisenberg), or of consensus parameters (Eisenberg et al))
- a 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 a data file.
Usage
Here is a sample session with pepinfo
% pepinfo Plots simple amino acid properties in parallel Input 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 Sequence USA
-graph xygraph Graph type
[-outfile] outfile Output file name
Additional (Optional) qualifiers:
-aaproperties datafile Amino acid properties filename
-aahydropathy datafile Hydropathy data filename
-hwindow integer Window size for hydropathy averaging
Advanced (Unprompted) qualifiers:
-[no]generalplot boolean Plot histogram of general properties
-[no]hydropathyplot boolean 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
-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 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 deaths
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| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (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, xml | EMBOSS_GRAPHICS value, or x11 |
| [-outfile] (Parameter 2) |
Output file name | Output file | <sequence>.pepinfo |
| Additional (Optional) qualifiers | Allowed values | Default | |
| -aaproperties | Amino acid properties filename | Data file | Eaa_properties.dat |
| -aahydropathy | Hydropathy data filename | 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 STANDARD; PRT; 348 AA.
AC P08100; Q16414;
DT 01-AUG-1988 (Rel. 08, Created)
DT 01-AUG-1988 (Rel. 08, Last sequence update)
DT 15-JUL-1999 (Rel. 38, Last annotation update)
DE RHODOPSIN.
GN RHO.
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
OC Eutheria; Primates; Catarrhini; Hominidae; Homo.
RN [1]
RP SEQUENCE FROM N.A.
RX MEDLINE; 84272729.
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 SEQUENCE OF 1-120 FROM N.A.
RA BENNETT J., BELLER B., SUN D., KARIKO K.;
RL Submitted (NOV-1994) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP REVIEW ON ADRP VARIANTS.
RX MEDLINE; 94004905.
RA AL-MAGHTHEH M., GREGORY C., INGLEHEARN C., HARDCASTLE A.,
RA BHATTACHARYA S.;
RT "Rhodopsin mutations in autosomal dominant retinitis pigmentosa.";
RL Hum. Mutat. 2:249-255(1993).
RN [4]
RP VARIANT ADRP HIS-23.
RX MEDLINE; 90136922.
RA DRYJA T.P., MCGEE T.L., REICHEI E., HAHN L.B., COWLEY G.S.,
RA YANDELL D.W., SANDBERG M.A., BERSON E.L.;
RT "A point mutation of the rhodopsin gene in one form of retinitis
RT pigmentosa.";
RL Nature 343:364-366(1990).
RN [5]
RP VARIANTS ADRP.
RX MEDLINE; 91051574.
RA FARRAR G.J., KENNA P., REDMOND R., MCWILLIAM P., BRADLEY D.G.,
RA HUMPHRIES M.M., SHARP E.M., INGLEHEARN C.F., BASHIR R., JAY M.,
RA WATTY A., LUDWIG M., SCHINZEL A., SAMANNS C., GAL A.,
RA BHATTACHARYA S.S., HUMPHRIES P.;
RT "Autosomal dominant retinitis pigmentosa: absence of the rhodopsin
RT proline-->histidine substitution (codon 23) in pedigrees from
RT Europe.";
RL Am. J. Hum. Genet. 47:941-945(1990).
RN [6]
RP VARIANTS ADRP HIS-23; ARG-58; LEU-347 AND SER-347.
RX MEDLINE; 91015273.
[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 ADRP).
FT /FTId=VAR_004818.
FT VARIANT 211 211 H -> R (IN ADRP).
FT /FTId=VAR_004819.
FT VARIANT 216 216 M -> K (IN ADRP).
FT /FTId=VAR_004820.
FT VARIANT 220 220 F -> C (IN ADRP).
FT /FTId=VAR_004821.
FT VARIANT 222 222 C -> R (IN ADRP).
FT /FTId=VAR_004822.
FT VARIANT 255 255 MISSING (IN ADRP).
FT /FTId=VAR_004823.
FT VARIANT 264 264 MISSING (IN ADRP).
FT /FTId=VAR_004824.
FT VARIANT 267 267 P -> L (IN ADRP).
FT /FTId=VAR_004825.
FT VARIANT 267 267 P -> R (IN ADRP).
FT /FTId=VAR_004826.
FT VARIANT 292 292 A -> E (IN CSNB4).
FT /FTId=VAR_004827.
FT VARIANT 296 296 K -> E (IN ADRP).
FT /FTId=VAR_004828.
FT VARIANT 297 297 S -> R (IN ADRP).
FT /FTId=VAR_004829.
FT VARIANT 342 342 T -> M (IN ADRP).
FT /FTId=VAR_004830.
FT VARIANT 345 345 V -> L (IN ADRP).
FT /FTId=VAR_004831.
FT VARIANT 345 345 V -> M (IN ADRP).
FT /FTId=VAR_004832.
FT VARIANT 347 347 P -> A (IN ADRP).
FT /FTId=VAR_004833.
FT VARIANT 347 347 P -> L (IN ADRP; COMMON VARIANT).
FT /FTId=VAR_004834.
FT VARIANT 347 347 P -> Q (IN ADRP).
FT /FTId=VAR_004835.
FT VARIANT 347 347 P -> R (IN ADRP).
FT /FTId=VAR_004836.
FT VARIANT 347 347 P -> S (IN ADRP).
FT /FTId=VAR_004837.
SQ SEQUENCE 348 AA; 38892 MW; 07443BEA CRC32;
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
//
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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
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Graphics File: pepinfo.ps
![[pepinfo results]](pepinfo.1.pepinfo.gif)
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
None.References
- 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
- 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
- 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 |
|---|---|
| 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 |
| 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 |
Author(s)
Mark Faller (current e-mail address unknown)while he was with:
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK