eprop |
Please help by correcting and extending the Wiki pages.
% eprop Reports propeptide cleavage sites in proteins Input (aligned) protein sequence set: EDA_HUMAN.fsa Output file [eda_human.eprop]: |
Go to the input files for this example
Go to the output files for this example
Reports propeptide cleavage sites in proteins Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] seqset (Aligned) protein sequence set filename and optional format, or reference (input USA) [-outfile] outfile [*.eprop] Output file name Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -plot boolean [N] Produce graphics -pcprediction boolean [N] Perform proprotein convertase prediction -signalp boolean [N] Include signal peptide cleavage site prediction Associated qualifiers: "-sequence" 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 "-outfile" associated qualifiers -odirectory2 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 |
Qualifier | Type | Description | Allowed values | Default |
---|---|---|---|---|
Standard (Mandatory) qualifiers | ||||
[-sequence] (Parameter 1) |
seqset | (Aligned) protein sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required |
[-outfile] (Parameter 2) |
outfile | Output file name | Output file | <*>.eprop |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-plot | boolean | Produce graphics | Boolean value Yes/No | No |
-pcprediction | boolean | Perform proprotein convertase prediction | Boolean value Yes/No | No |
-signalp | boolean | Include signal peptide cleavage site prediction | Boolean value Yes/No | No |
Associated qualifiers | ||||
"-sequence" associated seqset qualifiers | ||||
-sbegin1 -sbegin_sequence |
integer | Start of each sequence to be used | Any integer value | 0 |
-send1 -send_sequence |
integer | End of each sequence to be used | Any integer value | 0 |
-sreverse1 -sreverse_sequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
-sask1 -sask_sequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
-snucleotide1 -snucleotide_sequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
-sprotein1 -sprotein_sequence |
boolean | Sequence is protein | Boolean value Yes/No | N |
-slower1 -slower_sequence |
boolean | Make lower case | Boolean value Yes/No | N |
-supper1 -supper_sequence |
boolean | Make upper case | Boolean value Yes/No | N |
-sformat1 -sformat_sequence |
string | Input sequence format | Any string | |
-sdbname1 -sdbname_sequence |
string | Database name | Any string | |
-sid1 -sid_sequence |
string | Entryname | Any string | |
-ufo1 -ufo_sequence |
string | UFO features | Any string | |
-fformat1 -fformat_sequence |
string | Features format | Any string | |
-fopenfile1 -fopenfile_sequence |
string | Features file name | Any string | |
"-outfile" associated outfile qualifiers | ||||
-odirectory2 -odirectory_outfile |
string | Output directory | Any string | |
General qualifiers | ||||
-auto | boolean | Turn off prompts | Boolean value Yes/No | N |
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
-warning | boolean | Report warnings | Boolean value Yes/No | Y |
-error | boolean | Report errors | Boolean value Yes/No | Y |
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
-die | boolean | Report dying program messages | Boolean value Yes/No | Y |
-version | boolean | Report version number and exit | Boolean value Yes/No | N |
>EDA_HUMAN Q92838 Ectodysplasin A (Ectodermal dysplasia protein) (EDA protein). - Homo sapiens (Human). MGYPEVERRELLPAAAPRERGSQGCGCGGAPARAGEGNSCLLFLGFFGLSLALHLLTLCC YLELRSELRRERGAESRLGGSGTPGTSGTLSSLGGLDPDSPITSHLGQPSPKQQPLEPGE AALHSDSQDGHQMALLNFFFPDEKPYSEEESRRVRRNKRSKSNEGADGPVKNKKKGKKAG PPGPNGPPGPPGPPGPQGPPGIPGIPGIPGTTVMGPPGPPGPPGPQGPPGLQGPSGAADK AGTRENQPAVVHLQGQGSAIQVKNDLSGGVLNDWSRITMNPKVFKLHPRSGELEVLVDGT YFIYSQVEVYYINFTDFASYEVVVDEKPFLQCTRSIETGKTNYNTCYTAGVCLLKARQKI AVKMVHADISINMSKHTTFFGAIRLGEAPAS |
##### ProP v.1.0b ProPeptide Cleavage Site Prediction ##### ##### Furin-type cleavage site prediction (Arginine/Lysine residues) ##### 391 EDA_HUMAN MGYPEVERRELLPAAAPRERGSQGCGCGGAPARAGEGNSCLLFLGFFGLSLALHLLTLCCYLELRSELRRERGAESRLGG 80 SGTPGTSGTLSSLGGLDPDSPITSHLGQPSPKQQPLEPGEAALHSDSQDGHQMALLNFFFPDEKPYSEEESRRVRRNKRS 160 KSNEGADGPVKNKKKGKKAGPPGPNGPPGPPGPPGPQGPPGIPGIPGIPGTTVMGPPGPPGPPGPQGPPGLQGPSGAADK 240 AGTRENQPAVVHLQGQGSAIQVKNDLSGGVLNDWSRITMNPKVFKLHPRSGELEVLVDGTYFIYSQVEVYYINFTDFASY 320 EVVVDEKPFLQCTRSIETGKTNYNTCYTAGVCLLKARQKIAVKMVHADISINMSKHTTFFGAIRLGEAPAS 400 ................................................................................ 80 ..............................................................................P. 160 ................................................................................ 240 ................................................................................ 320 ....................................................................... 400 Propeptide cleavage sites predicted: Arg(R)/Lys(K): 1 Name Pos Context Score Pred ____________________________v_________________ EDA_HUMAN 8 GYPEVER|RE 0.057 . EDA_HUMAN 9 YPEVERR|EL 0.128 . EDA_HUMAN 18 LPAAAPR|ER 0.135 . EDA_HUMAN 20 AAAPRER|GS 0.102 . EDA_HUMAN 33 CGGAPAR|AG 0.090 . EDA_HUMAN 65 CCYLELR|SE 0.089 . EDA_HUMAN 69 ELRSELR|RE 0.081 . EDA_HUMAN 70 LRSELRR|ER 0.195 . EDA_HUMAN 72 SELRRER|GA 0.293 . EDA_HUMAN 77 ERGAESR|LG 0.112 . EDA_HUMAN 112 LGQPSPK|QQ 0.064 . EDA_HUMAN 144 FFFPDEK|PY 0.060 . EDA_HUMAN 152 YSEEESR|RV 0.096 . EDA_HUMAN 153 SEEESRR|VR 0.114 . EDA_HUMAN 155 EESRRVR|RN 0.204 . EDA_HUMAN 156 ESRRVRR|NK 0.482 . EDA_HUMAN 158 RRVRRNK|RS 0.182 . EDA_HUMAN 159 RVRRNKR|SK 0.819 *ProP* EDA_HUMAN 161 RRNKRSK|SN 0.131 . EDA_HUMAN 171 GADGPVK|NK 0.060 . EDA_HUMAN 173 DGPVKNK|KK 0.066 . EDA_HUMAN 174 GPVKNKK|KG 0.119 . EDA_HUMAN 175 PVKNKKK|GK 0.156 . EDA_HUMAN 177 KNKKKGK|KA 0.116 . EDA_HUMAN 178 NKKKGKK|AG 0.120 . EDA_HUMAN 240 PSGAADK|AG 0.060 . EDA_HUMAN 244 ADKAGTR|EN 0.082 . EDA_HUMAN 263 GSAIQVK|ND 0.066 . EDA_HUMAN 276 VLNDWSR|IT 0.077 . EDA_HUMAN 282 RITMNPK|VF 0.057 . EDA_HUMAN 285 MNPKVFK|LH 0.064 . EDA_HUMAN 289 VFKLHPR|SG 0.116 . EDA_HUMAN 327 EVVVDEK|PF 0.060 . EDA_HUMAN 334 PFLQCTR|SI 0.152 . EDA_HUMAN 340 RSIETGK|TN 0.061 . EDA_HUMAN 355 AGVCLLK|AR 0.059 . EDA_HUMAN 357 VCLLKAR|QK 0.099 . EDA_HUMAN 359 LLKARQK|IA 0.073 . EDA_HUMAN 363 RQKIAVK|MV 0.078 . EDA_HUMAN 375 ISINMSK|HT 0.067 . EDA_HUMAN 384 TFFGAIR|LG 0.076 . ____________________________^_________________ |
Program name | Description |
---|---|
enetnglyc | Reports N-glycosylation sites in human proteins |
enetoglyc | Reports mucin type GalNAc O-glycosylation sites in mammalian proteins |
enetphos | Reports ser, thr and tyr phosphorylation sites in eukaryotic proteins |
esignalp | Reports protein signal cleavage sites |
eyinoyang | Reports O-(beta)-GlcNAc attachment sites |
The original CBS group application must be licensed and installed to use this wrapper.
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.