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enetoglyc |
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% enetoglyc Reports mucin type GalNAc O-glycosylation sites in mammalian proteins Input (aligned) protein sequence set: LEUK_RAT.fsa Output file [leuk_rat.enetoglyc]: |
Go to the input files for this example
Go to the output files for this example
Reports mucin type GalNAc O-glycosylation sites in mammalian proteins
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-sequence] seqset (Aligned) protein sequence set filename and
optional format, or reference (input USA)
[-outfile] outfile [*.enetoglyc] Output file name
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-plot boolean [N] Produce graphics
-signalp boolean [N] Run signalp on the sequences
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
-scircular1 boolean Sequence is circular
-squick1 boolean Read id and sequence only
-sformat1 string Input sequence format
-iquery1 string Input query fields or ID list
-ioffset1 integer Input start position offset
-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 | <*>.enetoglyc |
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| -plot | boolean | Produce graphics | Boolean value Yes/No | No |
| -signalp | boolean | Run signalp on the sequences | 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 |
| -scircular1 -scircular_sequence |
boolean | Sequence is circular | Boolean value Yes/No | N |
| -squick1 -squick_sequence |
boolean | Read id and sequence only | Boolean value Yes/No | N |
| -sformat1 -sformat_sequence |
string | Input sequence format | Any string | |
| -iquery1 -iquery_sequence |
string | Input query fields or ID list | Any string | |
| -ioffset1 -ioffset_sequence |
integer | Input start position offset | Any integer value | 0 |
| -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 |
>LEUK_RAT P13838 LEUKOSIALIN PRECURSOR (LEUCOCYTE SIALOGLYCOPROTEIN) (SIALOPHORIN) (CD43) (W3/13 ANTIGEN) (FRAGMENT). - RATTUS NORVEGICUS (RAT). WAQVVSQENLPNTMTMLPFTPNSESPSTSEALSTYSSIATVPVTEDPKESISPWGQTTAP ASSIPLGTPELSSFFFTSAGASGNTPVPELTTSQEVSTEASLVLFPKSSGVASDPPVTIT NPATSSAVASTSLETFKGTSAPPVTVTSSTMTSGPFVATTVSSETSGPPVTMATGSLGPS KETHGLSATIATSSGESSSVAGGTPVFSTKISTTSTPNPITTVPPRPGSSGMLLVSMLIA LTVVLVLVALLLLWRQRQKRRTGALTLSRGGKRNGTVDAWAGPARVPDEEATTASGSGGN KSSGAPETDGSGQRPTLTTFFSRRKSRQGSVALEELKPGTGPNLKGEEEPLVGSEDEAVE TPTSDGPQAKDGAAPQSL |
Name: LEUK_RAT Length: 378 WAQVVSQENLPNTMTMLPFTPNSESPSTSEALSTYSSIATVPVTEDPKESISPWGQTTAPASSIPLGTPELSSFFFTSAG ASGNTPVPELTTSQEVSTEASLVLFPKSSGVASDPPVTITNPATSSAVASTSLETFKGTSAPPVTVTSSTMTSGPFVATT VSSETSGPPVTMATGSLGPSKETHGLSATIATSSGESSSVAGGTPVFSTKISTTSTPNPITTVPPRPGSSGMLLVSMLIA LTVVLVLVALLLLWRQRQKRRTGALTLSRGGKRNGTVDAWAGPARVPDEEATTASGSGGNKSSGAPETDGSGQRPTLTTF FSRRKSRQGSVALEELKPGTGPNLKGEEEPLVGSEDEAVETPTSDGPQAKDGAAPQSL ..............T....T....S.STS...ST.SS..T...T.....S.S....TT.........T....S...T... ....T.....TT.....T..............S....T.T...TSS...STS..T...TS....T.TSST.TS.....TT .SS.TS....T..T.S...S..T.....T..TSS...SS....T...ST..STTST....TT.................. ...................................................TT.S.S....SS....T.......T.... ........................................T.T.............S. Name S/T Pos G-score I-score Y/N Comment ---------------------------------------------------------------------------- LEUK_RAT S 6 0.379 0.054 . - LEUK_RAT T 13 0.498 0.039 . - LEUK_RAT T 15 0.535 0.095 T - LEUK_RAT T 20 0.567 0.070 T - LEUK_RAT S 23 0.469 0.059 . - LEUK_RAT S 25 0.502 0.029 S - LEUK_RAT S 27 0.526 0.190 S - LEUK_RAT T 28 0.659 0.100 T - LEUK_RAT S 29 0.552 0.153 S - LEUK_RAT S 33 0.567 0.035 S - LEUK_RAT T 34 0.650 0.097 T - LEUK_RAT S 36 0.557 0.047 S - LEUK_RAT S 37 0.550 0.046 S - LEUK_RAT T 40 0.653 0.087 T - LEUK_RAT T 44 0.609 0.408 T - LEUK_RAT S 50 0.565 0.065 S - LEUK_RAT S 52 0.554 0.053 S - LEUK_RAT T 57 0.669 0.045 T - LEUK_RAT T 58 0.661 0.050 T - LEUK_RAT S 62 0.477 0.084 . - LEUK_RAT S 63 0.457 0.277 . - LEUK_RAT T 68 0.576 0.081 T - LEUK_RAT S 72 0.497 0.040 . - LEUK_RAT S 73 0.503 0.034 S - LEUK_RAT T 77 0.592 0.054 T - LEUK_RAT S 78 0.466 0.050 . - LEUK_RAT S 82 0.459 0.163 . - LEUK_RAT T 85 0.562 0.110 T - LEUK_RAT T 91 0.592 0.072 T - LEUK_RAT T 92 0.577 0.152 T - LEUK_RAT S 93 0.451 0.065 . - LEUK_RAT S 97 0.454 0.048 . - LEUK_RAT T 98 0.570 0.190 T - LEUK_RAT S 101 0.498 0.029 . - LEUK_RAT S 108 0.461 0.048 . - LEUK_RAT S 109 0.465 0.043 . - [Part of this file has been deleted for brevity] LEUK_RAT S 180 0.516 0.121 S - LEUK_RAT T 183 0.633 0.077 T - LEUK_RAT S 187 0.492 0.039 . - LEUK_RAT T 189 0.608 0.202 T - LEUK_RAT T 192 0.597 0.255 T - LEUK_RAT S 193 0.520 0.033 S - LEUK_RAT S 194 0.526 0.033 S - LEUK_RAT S 197 0.478 0.037 . - LEUK_RAT S 198 0.501 0.031 S - LEUK_RAT S 199 0.503 0.104 S - LEUK_RAT T 204 0.696 0.099 T - LEUK_RAT S 208 0.600 0.078 S - LEUK_RAT T 209 0.700 0.298 T - LEUK_RAT S 212 0.615 0.041 S - LEUK_RAT T 213 0.707 0.070 T - LEUK_RAT T 214 0.712 0.644 T - LEUK_RAT S 215 0.613 0.046 S - LEUK_RAT T 216 0.711 0.609 T - LEUK_RAT T 221 0.670 0.193 T - LEUK_RAT T 222 0.650 0.465 T - LEUK_RAT S 229 0.428 0.064 . - LEUK_RAT S 230 0.379 0.056 . - LEUK_RAT S 236 0.215 0.053 . - LEUK_RAT T 242 0.113 0.093 . - LEUK_RAT T 262 0.193 0.055 . - LEUK_RAT T 266 0.228 0.060 . - LEUK_RAT S 268 0.201 0.073 . - LEUK_RAT T 276 0.402 0.045 . - LEUK_RAT T 292 0.603 0.232 T - LEUK_RAT T 293 0.616 0.413 T - LEUK_RAT S 295 0.507 0.098 S - LEUK_RAT S 297 0.533 0.047 S - LEUK_RAT S 302 0.520 0.038 S - LEUK_RAT S 303 0.503 0.038 S - LEUK_RAT T 308 0.577 0.208 T - LEUK_RAT S 311 0.385 0.072 . - LEUK_RAT T 316 0.506 0.221 T - LEUK_RAT T 318 0.496 0.070 . - LEUK_RAT T 319 0.469 0.045 . - LEUK_RAT S 322 0.254 0.055 . - LEUK_RAT S 326 0.292 0.024 . - LEUK_RAT S 330 0.288 0.047 . - LEUK_RAT T 340 0.422 0.058 . - LEUK_RAT S 354 0.463 0.034 . - LEUK_RAT T 361 0.594 0.214 T - LEUK_RAT T 363 0.598 0.403 T - LEUK_RAT S 364 0.492 0.463 . - LEUK_RAT S 377 0.579 0.021 S - ---------------------------------------------------------------------------- |
| Program name | Description |
|---|---|
| enetnglyc | Report N-glycosylation sites in human proteins |
| enetphos | Report Ser, Thr and Tyr phosphorylation sites in eukaryotic proteins |
| eprop | Report propeptide cleavage sites in proteins |
| esignalp | Report protein signal cleavage sites |
| eyinoyang | Report 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.