pepinfo Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. 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:6.4.0.0 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 -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 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 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 15-JUN-2010, entry version 128. 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: * . (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 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 Draws circular maps 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 Draws 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 Reports on protein proteolytic enzyme or reagent cleavage sites pepnet Draw a helical net for a protein sequence pepstats Calculates 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 Displays 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 (c) 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