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EMBOSS: digest |
% 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] outfile Output file name 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. -allpartials bool As for overlap but fragments containing more than one potential cut site are included. |
Mandatory qualifiers | Allowed values | Default | |||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
[-sequencea] (Parameter 1) |
Sequence USA | Readable sequence | Required | ||||||||||||||||
-menu | Select number |
|
1 | ||||||||||||||||
[-outfile] (Parameter 2) |
Output file name | Output file | <sequence>.digest | ||||||||||||||||
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 | ||||||||||||||||
-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 |
---|---|
checktrans | Reports STOP codons and ORF statistics of a protein sequence |
iep | Calculates the isoelectric point of a protein |
octanol | Displays protein hydropathy |
pepinfo | Plots simple amino acid properties in parallel |
pepnet | Displays proteins as a helical net |
pepstats | Protein statistics |
pepwheel | Shows protein sequences as helices |
pepwindow | Displays protein hydropathy |
pepwindowall | Displays protein hydropathy of a set of sequences |