hmoment 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 Calculate and plot hydrophobic moment for protein sequence(s) Description hmoment plots or writes out the hydrophobic moment calculated for overlapping windows over one or more input protein sequences. The hydrophic moment reflects the periodicity of hydrophobicity of a peptide, as measured per residue for a specified angle of rotation. The window size, alpha helix angle, and beta sheet angle are user-specified. The alpha helix moment and beta sheet moment may be plotted or output. Algorithm The hydrophobic moment is measured within a moving window using the method of Eisenberg et al. The default angle of 100 degrees is used for the alpha-helix results and the default of 160 degrees is used for the beta-sheet results. These angles can be changed if required using the appropriate options. Usage Here is a sample session with hmoment % hmoment tsw:hbb_human Calculate and plot hydrophobic moment for protein sequence(s) Output file [hbb_human.hmoment]: Go to the input files for this example Go to the output files for this example Command line arguments Calculate and plot hydrophobic moment for protein sequence(s) Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers (* if not always prompted): [-seqall] seqall Protein sequence(s) 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 [*.hmoment] Output file name Additional (Optional) qualifiers: -window integer [10] Window (Any integer value) -aangle integer [100] Alpha helix angle (degrees) (Any integer value) -bangle integer [160] Beta sheet angle (degrees) (Any integer value) Advanced (Unprompted) qualifiers: -baseline float [0.35] Graph marker line (Any numeric value) -plot toggle [N] Produce graphic -double boolean [N] Plot two graphs Associated qualifiers: "-seqall" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each 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 -odirectory 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 hmoment reads one or protein sequences. 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:hbb_human' is a sequence entry in the example protein database 'tsw' Database entry: tsw:hbb_human ID HBB_HUMAN Reviewed; 147 AA. AC P68871; A4GX73; B2ZUE0; P02023; Q13852; Q14481; Q14510; Q45KT0; AC Q549N7; Q6FI08; Q6R7N2; Q8IZI1; Q9BX96; Q9UCD6; Q9UCP8; Q9UCP9; DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot. DT 23-JAN-2007, sequence version 2. DT 15-JUN-2010, entry version 88. DE RecName: Full=Hemoglobin subunit beta; DE AltName: Full=Hemoglobin beta chain; DE AltName: Full=Beta-globin; DE Contains: DE RecName: Full=LVV-hemorphin-7; GN Name=HBB; 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=77126403; PubMed=1019344; RA Marotta C., Forget B., Cohen-Solal M., Weissman S.M.; RT "Nucleotide sequence analysis of coding and noncoding regions of human RT beta-globin mRNA."; RL Prog. Nucleic Acid Res. Mol. Biol. 19:165-175(1976). RN [2] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RX MEDLINE=81064667; PubMed=6254664; DOI=10.1016/0092-8674(80)90428-6; RA Lawn R.M., Efstratiadis A., O'Connell C., Maniatis T.; RT "The nucleotide sequence of the human beta-globin gene."; RL Cell 21:647-651(1980). RN [3] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANT LYS-7. RX PubMed=16175509; DOI=10.1086/491748; RA Wood E.T., Stover D.A., Slatkin M., Nachman M.W., Hammer M.F.; RT "The beta-globin recombinational hotspot reduces the effects of strong RT selection around HbC, a recently arisen mutation providing resistance RT to malaria."; RL Am. J. Hum. Genet. 77:637-642(2005). RN [4] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RA Lu L., Hu Z.H., Du C.S., Fu Y.S.; RT "DNA sequence of the human beta-globin gene isolated from a healthy RT Chinese."; RL Submitted (JUN-1997) to the EMBL/GenBank/DDBJ databases. RN [5] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANT ARG-113. RA Cabeda J.M., Correia C., Estevinho A., Cardoso C., Amorim M.L., RA Cleto E., Vale L., Coimbra E., Pinho L., Justica B.; RT "Unexpected patterns of globin mutations in thalassemia patients from RT north of Portugal."; [Part of this file has been deleted for brevity] FT VARIANT 141 141 A -> V (in Puttelange; polycythemia; O(2) FT affinity up). FT /FTId=VAR_003082. FT VARIANT 142 142 L -> R (in Olmsted; unstable). FT /FTId=VAR_003083. FT VARIANT 143 143 A -> D (in Ohio; O(2) affinity up). FT /FTId=VAR_003084. FT VARIANT 144 144 H -> D (in Rancho Mirage). FT /FTId=VAR_003085. FT VARIANT 144 144 H -> P (in Syracuse; O(2) affinity up). FT /FTId=VAR_003087. FT VARIANT 144 144 H -> Q (in Little Rock; O(2) affinity FT up). FT /FTId=VAR_003086. FT VARIANT 144 144 H -> R (in Abruzzo; O(2) affinity up). FT /FTId=VAR_003088. FT VARIANT 145 145 K -> E (in Mito; O(2) affinity up). FT /FTId=VAR_003089. FT VARIANT 146 146 Y -> C (in Rainier; O(2) affinity up). FT /FTId=VAR_003090. FT VARIANT 146 146 Y -> H (in Bethesda; O(2) affinity up). FT /FTId=VAR_003091. FT VARIANT 147 147 H -> D (in Hiroshima; O(2) affinity up). FT /FTId=VAR_003092. FT VARIANT 147 147 H -> L (in Cowtown; O(2) affinity up). FT /FTId=VAR_003093. FT VARIANT 147 147 H -> P (in York; O(2) affinity up). FT /FTId=VAR_003094. FT VARIANT 147 147 H -> Q (in Kodaira; O(2) affinity up). FT /FTId=VAR_003095. FT CONFLICT 26 26 Missing (in Ref. 15; ACD39349). FT CONFLICT 42 42 F -> L (in Ref. 13; AAR96398). FT HELIX 6 16 FT TURN 21 23 FT HELIX 24 35 FT HELIX 37 42 FT HELIX 44 46 FT HELIX 52 57 FT HELIX 59 77 FT TURN 78 80 FT HELIX 82 94 FT TURN 95 97 FT HELIX 102 119 FT HELIX 120 122 FT HELIX 125 142 FT HELIX 144 146 SQ SEQUENCE 147 AA; 15998 MW; A31F6D621C6556A1 CRC64; MVHLTPEEKS AVTALWGKVN VDEVGGEALG RLLVVYPWTQ RFFESFGDLS TPDAVMGNPK VKAHGKKVLG AFSDGLAHLD NLKGTFATLS ELHCDKLHVD PENFRLLGNV LVCVLAHHFG KEFTPPVQAA YQKVVAGVAN ALAHKYH // Output file format With the '-plot' option hmoment displays a graphical plot of the hydrophobic moment of the specified alpha helix angle. With the '-plot -double' options it also displays the beta-sheet hydrophobic moment. 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. Otherwise it writes out a files containing the two columns separated by space or TAB characters. The first column is the position of the start of the window that the hydrophobic moment was calculated in. The second is the hydrophobic moment ('uH'). (If the option '-double' is given then the beta-sheet angle hydrophobicity is given as a third column.) Output files for usage example File: hbb_human.hmoment HMOMENT of HBB_HUMAN from 1 to 147 Window: 10 Angle: 100 Max uH: 0.714 Position uH 1 0.086 2 0.091 3 0.216 4 0.208 5 0.123 6 0.211 7 0.194 8 0.185 9 0.169 10 0.312 11 0.292 12 0.185 13 0.092 14 0.050 15 0.164 16 0.245 17 0.187 18 0.130 19 0.262 20 0.396 21 0.317 22 0.342 23 0.492 24 0.508 25 0.517 26 0.418 27 0.416 28 0.350 29 0.292 30 0.196 31 0.102 32 0.288 33 0.314 34 0.442 35 0.560 36 0.464 37 0.577 38 0.584 39 0.676 40 0.714 41 0.670 42 0.462 43 0.369 44 0.221 45 0.176 46 0.073 [Part of this file has been deleted for brevity] 88 0.179 89 0.201 90 0.065 91 0.041 92 0.110 93 0.181 94 0.261 95 0.312 96 0.200 97 0.263 98 0.369 99 0.310 100 0.362 101 0.495 102 0.585 103 0.450 104 0.488 105 0.547 106 0.315 107 0.311 108 0.252 109 0.187 110 0.215 111 0.295 112 0.425 113 0.303 114 0.421 115 0.528 116 0.487 117 0.436 118 0.501 119 0.532 120 0.409 121 0.447 122 0.308 123 0.383 124 0.252 125 0.361 126 0.374 127 0.314 128 0.219 129 0.310 130 0.361 131 0.439 132 0.433 133 0.507 134 0.336 135 0.344 136 0.207 137 0.234 138 0.299 Data files None. Notes When proteins of known three-dimensional structure are examined, it is found that sequences that form alpha helices tend to have, on average, a strong periodicity in the hydrophobicity of af 3.6 residues, the period of the alpha helix. The angle of rotation per residue in alpha helices is 100 degrees. Similarly, many sequences that form strands of beta sheets tend to have a periodicity in their hydrophobicity of about 2.3 residues, the period typical of beta structure. The angle of rotation per residue in beta sheets is 160 degrees. This means that many protein sequences tend to form the periodic structure that maximizes their amphiphilicity. Periodicities in the polar/apolar character of the amino acid sequence of a protein can be examined by assigning to each residue a numerical hydrophobicity and searching for periodicity in the resulting one-dimensional function. The strength of each periodic component is the quantity that has been termed the hydrophobic moment. The -plot option must be specified to produce a plot. hmoment can plot two graphs when the option -double is given, one for the alpha helix moment and one for the beta sheet moment. Otherwise it just plots the alpha helix moment. References 1. Eisenberg D, Weiss RM, Terwilliger TC "The hydrophobic moment detects periodicity in protein hydrophobicity." Proc Natl Acad Sci U S A 1984 Jan;81(1):140-4 Warnings None. Diagnostic Error Messages None. Exit status It always exits with status 0. Known bugs None. See also Program name Description charge Draw a protein charge plot iep Calculate the isoelectric point of proteins octanol Draw a White-Wimley protein hydropathy plot pepinfo Plot amino acid properties of a protein sequence in parallel pepstats Calculates statistics of protein properties pepwindow Draw a hydropathy plot for a protein sequence pepwindowall Draw Kyte-Doolittle hydropathy plot for a protein alignment Author(s) Alan Bleasby European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Written (March 2001) - Alan Bleasby. Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None