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EMBOSS: 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 list Select number [-outfile] report (no help text) report value Optional qualifiers: (none) Advanced qualifiers: -unfavoured bool 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. -overlap bool 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. -aadata string Molecular weight data for amino acids -allpartials bool As for overlap but fragments containing more than one potential cut site are included. 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 | |||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
[-sequencea] (Parameter 1) |
Sequence USA | Readable sequence | Required | ||||||||||||||||
-menu | Select number |
|
1 | ||||||||||||||||
[-outfile] (Parameter 2) |
(no help text) report value | 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 | ||||||||||||||||
-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 | ||||||||||||||||
-aadata | Molecular weight data for amino acids | Any string is accepted | Eamino.dat | ||||||||||||||||
-allpartials | As for overlap but fragments containing more than one potential cut site are included. | Yes/No | No |
DIGEST of OPSD_HUMAN from 1 to 348 Molwt= 38892.536 Complete digestion with Trypsin yields 14 fragments: Start End Molwt Sequence (up to 38 residues) 70 135 7129.324 (R) TPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGP (Y) ... 178 231 6335.500 (R) YIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIP (E) ... 22 69 5788.878 (R) SPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTL (T) ... 253 296 5004.090 (R) MVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTI (S) ... 136 177 4600.464 (R) YVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLA (Y) ... 1 21 2257.500 () MNGTEGPNFYVPFSNATGVVR (S) 297 311 1728.093 (K) SAAIYNPVIYIMMNK (Q) 232 245 1490.543 (K) EAAAQQQESATTQK (A) 326 339 1403.462 (K) NPLGDDEASATVSK (T) 315 325 1186.480 (R) NCMLTTICCGK (N) 340 348 902.954 (K) TETSQVAPA () 249 252 503.555 (K) EVTR (M) 312 314 449.509 (K) QFR (N) 246 248 346.383 (K) AEK (E)
The first non-blank line is the title containing the name of the program and the name o fthe input sequence with the range considered and the calculated molecular weight of the protein.
The next non-blank line gives the name of the reagent used to digest the protein and the number of fragments reported. The line will report is complete or partial digestion was chosen. If the protein is not digested at all by the reagent chosen the following is reported:
"Is not proteolytically digested using (reagent name)"
If '-overlap' was specified, the next line will be:
"Only overlapping partials shown:"
If '-allpartials' was specified, the next line will be:
"All partials shown:"
The next non-blank line gives the headings of the columns of data.
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 |