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EMBOSS: charge |
% charge sw:hbb_human Protein charge plot Output file [hbb_human.charge]:
Mandatory qualifiers (* if not always prompted): [-seqall] seqall Sequence database USA * -graph xygraph Graph type * -outfile outfile Output file name Optional qualifiers: -window integer Window Advanced qualifiers: -aadata string Amino acid property data file name -plot bool Produce graphic General qualifiers: -help bool report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-seqall] (Parameter 1) |
Sequence database USA | Readable sequence(s) | 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 | EMBOSS_GRAPHICS value, or x11 |
-outfile | Output file name | Output file | <sequence>.charge |
Optional qualifiers | Allowed values | Default | |
-window | Window | Integer 1 or more | 5 |
Advanced qualifiers | Allowed values | Default | |
-aadata | Amino acid property data file name | Any string is accepted | Eamino.dat |
-plot | Produce graphic | Yes/No | No |
The output file contains two columns separated by space or TAB characters. The first column is the position of teh start of the window. The second column is the charge of the amino acids within that window.
The output of the example above is as follows:
CHARGE of HBB_HUMAN from 1 to 146: window 5 Position Charge 1 0.100 2 -0.100 3 -0.400 4 -0.200 5 -0.200 6 -0.200 7 0.000 8 0.200 9 0.000 10 0.000 11 0.000 12 0.000 13 0.200 14 0.200 15 0.200 16 0.200 17 0.000 18 -0.400 19 -0.400 20 -0.400 21 -0.400 22 -0.400 23 -0.200 24 -0.200 25 -0.200 26 0.000 27 0.200 28 0.200 29 0.200 30 0.200 31 0.000 32 0.000 33 0.000 34 0.000 35 0.000 36 0.200 37 0.200 38 0.200 39 0.000 40 0.000 41 -0.200 42 -0.200 43 -0.400 44 -0.200 45 -0.200 46 -0.200 47 -0.200 48 -0.200 49 -0.200 50 -0.200 51 -0.200 52 -0.200 53 0.000 54 0.000 55 0.200 56 0.200 57 0.400 58 0.400 59 0.500 60 0.300 61 0.500 62 0.500 63 0.500 64 0.400 65 0.400 66 0.200 67 0.000 68 0.000 69 -0.200 70 -0.200 71 -0.200 72 -0.200 73 -0.100 74 0.100 75 -0.100 76 -0.100 77 -0.100 78 0.000 79 0.000 80 0.200 81 0.200 82 0.200 83 0.000 84 0.000 85 0.000 86 -0.200 87 -0.200 88 -0.100 89 -0.100 90 -0.300 91 0.100 92 0.100 93 0.100 94 0.100 95 0.100 96 -0.100 97 -0.300 98 -0.400 99 -0.400 100 0.000 101 0.000 102 0.200 103 0.200 104 0.200 105 0.000 106 0.000 107 0.000 108 0.000 109 0.000 110 0.000 111 0.000 112 0.100 113 0.200 114 0.200 115 0.200 116 0.400 117 0.100 118 0.000 119 0.000 120 0.000 121 -0.200 122 0.000 123 0.000 124 0.000 125 0.000 126 0.000 127 0.000 128 0.200 129 0.200 130 0.200 131 0.200 132 0.200 133 0.000 134 0.000 135 0.000 136 0.000 137 0.000 138 0.000 139 0.100 140 0.300 141 0.300 142 0.400
EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.
To see the available EMBOSS data files, run:
% embossdata -showall
To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:
% embossdata -fetch -file Exxx.dat
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:
Program name | Description |
---|---|
backtranseq | Back translate a protein sequence |
checktrans | Reports STOP codons and ORF statistics of a protein sequence |
compseq | Counts the 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 |
mwfilter | Filter noisy molwts from mass spec output |
octanol | Displays protein hydropathy |
pepinfo | Plots simple amino acid properties in parallel |
pepstats | Protein statistics |
pepwindow | Displays protein hydropathy |
pepwindowall | Displays protein hydropathy of a set of sequences |