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digest |
This programs allows you to input a protein sequence and to specify one proteolytic agent from a list. It will then output a file containing the positions where the agent cuts, together with the peptides produced.
Trypsin will not normally cut after a K if it is followed by (e.g.) another K or a P. Specifying the qualifier -unfavoured shows those cuts. as well as the favoured ones.
If you wish to emulate a partial digestion, then using the -overlap qualifier will display the results from a digest in which all cut sites are used and in which one site at a time is not cut. Thus the resulting peptide fragments from the cut sites numbered 1, 2, 3, 4 etc. are shown, plus the fragments produced by cutting at the sites 1..3, 2..4, etc.
i.e. fragments containing one potential cut site are also shown.
If you wish to emulate a very partial digestion (!) then using the -allpartials qualifier will do what -overlap did, but also show all possible fragments from using all possible combinations of cut sites. For example, fragments from the cut sites numbered 1, 2, 3, 4, 5 and from the fragments produced by cutting between sites 1..3, 1..4, 1..5, 2..4, 2..5, 3..5, etc.
i.e. fragments containing one or more potential cut site are also shown.
% digest Input sequence: sw:opsd_human Enzymes and Reagents 1 : Trypsin 2 : Lys-C 3 : Arg-C 4 : Asp-N 5 : V8-bicarb 6 : V8-phosph 7 : Chymotrypsin 8 : CNBr Select number [1]: Output file [opsd_human.digest]:
Mandatory qualifiers: [-sequencea] sequence Sequence USA -menu menu Select number [-outfile] report Output report file name Optional qualifiers: (none) Advanced qualifiers: -unfavoured boolean Trypsin will not normally cut after a K if it is followed by (e.g.) another K or a P. Specifying this shows those cuts. as well as the favoured ones. -aadata string Molecular weight data for amino acids -overlap boolean Used for partial digestion. Shows all cuts from favoured cut sites plus 1..3, 2..4, 3..5 etc but not (e.g.) 2..5. Overlaps are therefore fragments with exactly one potential cut site within it. -allpartials boolean As for overlap but fragments containing more than one potential cut site are included. General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
[-sequencea] (Parameter 1) |
Sequence USA | Readable sequence | Required | ||||||||||||||||
-menu | Select number |
|
1 | ||||||||||||||||
[-outfile] (Parameter 2) |
Output report file name | Report file | |||||||||||||||||
Optional qualifiers | Allowed values | Default | |||||||||||||||||
(none) | |||||||||||||||||||
Advanced qualifiers | Allowed values | Default | |||||||||||||||||
-unfavoured | Trypsin will not normally cut after a K if it is followed by (e.g.) another K or a P. Specifying this shows those cuts. as well as the favoured ones. | Yes/No | No | ||||||||||||||||
-aadata | Molecular weight data for amino acids | Any string is accepted | Eamino.dat | ||||||||||||||||
-overlap | Used for partial digestion. Shows all cuts from favoured cut sites plus 1..3, 2..4, 3..5 etc but not (e.g.) 2..5. Overlaps are therefore fragments with exactly one potential cut site within it. | Yes/No | No | ||||||||||||||||
-allpartials | As for overlap but fragments containing more than one potential cut site are included. | Yes/No | No |
The output is a standard EMBOSS report file.
The results can be output in one of several styles by using the command-line qualifier -rformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, trace, listfile, dbmotif, diffseq, excel, feattable, motif, regions, seqtable, simple, srs, table, tagseq
See: http://www.uk.embnet.org/Software/EMBOSS/Themes/ReportFormats.html for further information on report formats.
By default digest writes a 'seqtable' report file.
######################################## # Program: digest # Rundate: Mon Feb 11 13:36:16 2002 # Report_file: opsd_human.digest ######################################## #======================================= # # Sequence: OPSD_HUMAN from: 1 to: 348 # HitCount: 14 # # Complete digestion with Trypsin yields 14 fragments # #======================================= Start End Mol_Weight cterm nterm Sequence 70 135 7129.319 R Y TPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIER 178 231 6335.495 R E YIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVK 22 69 5788.873 R T SPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLR 253 296 5004.085 R S MVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAK 136 177 4600.460 R Y YVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR 1 21 2257.495 . S MNGTEGPNFYVPFSNATGVVR 297 311 1728.089 K Q SAAIYNPVIYIMMNK 232 245 1490.538 K A EAAAQQQESATTQK 326 339 1403.457 K T NPLGDDEASATVSK 315 325 1186.476 R N NCMLTTICCGK 340 348 902.950 K . TETSQVAPA 249 252 503.550 K M EVTR 312 314 449.504 K N QFR 246 248 346.378 K E AEK #--------------------------------------- #---------------------------------------
The header information contains the propgram name, date of run, name of the reagent used to digest the protein and the number of fragments reported. The header will report if complete or partial digestion was chosen.
The rest of the file consists of columns holding the following data:
Program name | Description |
---|---|
antigenic | Finds antigenic sites in proteins |
fuzzpro | Protein pattern search |
fuzztran | Protein pattern search after translation |
helixturnhelix | Report nucleic acid binding motifs |
oddcomp | Finds protein sequence regions with a biased composition |
patmatdb | Search a protein sequence with a motif |
patmatmotifs | Search a PROSITE motif database with a protein sequence |
pepcoil | Predicts coiled coil regions |
preg | Regular expression search of a protein sequence |
pscan | Scans proteins using PRINTS |
sigcleave | Reports protein signal cleavage sites |