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eyinoyang |
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% eyinoyang Reports O-(beta)-GlcNAc attachment sites Input (aligned) sequence set: CBG_HUMAN.fsa Output file [cbg_human.eyinoyang]: |
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Go to the output files for this example
Example 2
% eyinoyang Reports O-(beta)-GlcNAc attachment sites Input (aligned) sequence set: LEUK_RAT.fsa Output file [leuk_rat.eyinoyang]: |
Go to the input files for this example
Go to the output files for this example
Reports O-(beta)-GlcNAc attachment sites
Version: EMBOSS:6.3.0
Standard (Mandatory) qualifiers:
[-sequence] seqset (Aligned) sequence set filename and optional
format, or reference (input USA)
[-outfile] outfile [*.eyinoyang] Output file name
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-plot boolean [N] Produce graphics
-format menu [short] Format (Values: short (short); long
(long))
-netphos boolean [N] Run netphos and predict Yin-Yang sites
-threshold float [0.5] Report netphos only scores above this
value (Number from 0.000 to 1.000)
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
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| Qualifier | Type | Description | Allowed values | Default | ||||
|---|---|---|---|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||||||
| [-sequence] (Parameter 1) |
seqset | (Aligned) sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required | ||||
| [-outfile] (Parameter 2) |
outfile | Output file name | Output file | <*>.eyinoyang | ||||
| Additional (Optional) qualifiers | ||||||||
| (none) | ||||||||
| Advanced (Unprompted) qualifiers | ||||||||
| -plot | boolean | Produce graphics | Boolean value Yes/No | No | ||||
| -format | list | Format |
|
short | ||||
| -netphos | boolean | Run netphos and predict Yin-Yang sites | Boolean value Yes/No | No | ||||
| -threshold | float | Report netphos only scores above this value | Number from 0.000 to 1.000 | 0.5 | ||||
| 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 | ||||
>CBG_HUMAN MPLLLYTCLLWLPTSGLWTVQAMDPNAAYVNMSNHHRGLASANVDFAFSLYKHLVALSPK KNIFISPVSISMALAMLSLGTCGHTRAQLLQGLGFNLTERSETEIHQGFQHLHQLFAKSD TSLEMTMGNALFLDGSLELLESFSADIKHYYESEVLAMNFQDWATASRQINSYVKNKTQG KIVDLFSGLDSPAILVLVNYIFFKGTWTQPFDLASTREENFYVDETTVVKVPMMLQSSTI SYLHDSELPCQLVQMNYVGNGTVFFILPDKGKMNTVIAALSRDTINRWSAGLTSSQVDLY IPKVTISGVYDLGDVLEEMGIADLFTNQANFSRITQDAQLKSSKVVHKAVLQLNEEGVDT AGSTGVTLNLTSKPIILRFNQPFIIMIFDHFTWSSLFLARVMNPV |
>LEUK_RAT P13838 LEUKOSIALIN PRECURSOR (LEUCOCYTE SIALOGLYCOPROTEIN) (SIALOPHORIN) (CD43) (W3/13 ANTIGEN) (FRAGMENT). - RATTUS NORVEGICUS (RAT). WAQVVSQENLPNTMTMLPFTPNSESPSTSEALSTYSSIATVPVTEDPKESISPWGQTTAP ASSIPLGTPELSSFFFTSAGASGNTPVPELTTSQEVSTEASLVLFPKSSGVASDPPVTIT NPATSSAVASTSLETFKGTSAPPVTVTSSTMTSGPFVATTVSSETSGPPVTMATGSLGPS KETHGLSATIATSSGESSSVAGGTPVFSTKISTTSTPNPITTVPPRPGSSGMLLVSMLIA LTVVLVLVALLLLWRQRQKRRTGALTLSRGGKRNGTVDAWAGPARVPDEEATTASGSGGN KSSGAPETDGSGQRPTLTTFFSRRKSRQGSVALEELKPGTGPNLKGEEEPLVGSEDEAVE TPTSDGPQAKDGAAPQSL |
The predictions for O-GlcNAc sites in 1 sequence
###############################################################################
Warning: This sequence seems to contain a signal peptide !!
Proteins with signal peptides are most probably secreted
and are unlikely to contain an O-(beta)-GlcNAc site
# SignalP-NN ver. 3.0 euk predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ? D ?
CBG_HUMAN 0.645 23 Y 0.717 23 Y 0.981 13 Y 0.886 Y 0.801 Y
###############################################################################
Name: CBG_HUMAN Length: 405
MPLLLYTCLLWLPTSGLWTVQAMDPNAAYVNMSNHHRGLASANVDFAFSLYKHLVALSPKKNIFISPVSISMALAMLSLG 80
TCGHTRAQLLQGLGFNLTERSETEIHQGFQHLHQLFAKSDTSLEMTMGNALFLDGSLELLESFSADIKHYYESEVLAMNF 160
QDWATASRQINSYVKNKTQGKIVDLFSGLDSPAILVLVNYIFFKGTWTQPFDLASTREENFYVDETTVVKVPMMLQSSTI 240
SYLHDSELPCQLVQMNYVGNGTVFFILPDKGKMNTVIAALSRDTINRWSAGLTSSQVDLYIPKVTISGVYDLGDVLEEMG 320
IADLFTNQANFSRITQDAQLKSSKVVHKAVLQLNEEGVDTAGSTGVTLNLTSKPIILRFNQPFIIMIFDHFTWSSLFLAR 400
VMNPV 480
..............G.....................................................G........... 80
................................................................................ 160
....G........................................................................... 240
................................................................G............... 320
.....................GG......................................................... 400
..... 480
----------------------------------------------------------
SeqName Residue O-GlcNAc Potential Thresh. Thresh.
result (1) (2)
----------------------------------------------------------
CBG_HUMAN 15 S + 0.4952 0.4560 0.5650
CBG_HUMAN 69 S + 0.5330 0.5116 0.6400
CBG_HUMAN 165 T + 0.5099 0.4381 0.5409
CBG_HUMAN 305 T ++ 0.5937 0.4585 0.5684
CBG_HUMAN 342 S ++ 0.4782 0.3860 0.4707
CBG_HUMAN 343 S + 0.4153 0.4096 0.5025
----------------------------------------------------------
|
The predictions for O-GlcNAc sites in 1 sequence
Name: LEUK_RAT Length: 378
WAQVVSQENLPNTMTMLPFTPNSESPSTSEALSTYSSIATVPVTEDPKESISPWGQTTAPASSIPLGTPELSSFFFTSAG 80
ASGNTPVPELTTSQEVSTEASLVLFPKSSGVASDPPVTITNPATSSAVASTSLETFKGTSAPPVTVTSSTMTSGPFVATT 160
VSSETSGPPVTMATGSLGPSKETHGLSATIATSSGESSSVAGGTPVFSTKISTTSTPNPITTVPPRPGSSGMLLVSMLIA 240
LTVVLVLVALLLLWRQRQKRRTGALTLSRGGKRNGTVDAWAGPARVPDEEATTASGSGGNKSSGAPETDGSGQRPTLTTF 320
FSRRKSRQGSVALEELKPGTGPNLKGEEEPLVGSEDEAVETPTSDGPQAKDGAAPQSL 400
.....G.............G..G....GG...G..........G.....G......GG...GG................. 80
..........GGG...GG.........GG........G.G...GGG....G.............G.GGG...G.....G. 160
.GG..G....G...........G........GGG...G.........G.....G......GG......G........... 240
.....................G.............................GG.G............G.........G.. 320
...........................................G............G. 400
----------------------------------------------------------
SeqName Residue O-GlcNAc Potential Thresh. Thresh.
result (1) (2)
----------------------------------------------------------
LEUK_RAT 6 S ++ 0.5334 0.4196 0.5159
LEUK_RAT 20 T + 0.4550 0.4247 0.5229
LEUK_RAT 23 S +++ 0.6551 0.3665 0.4444
LEUK_RAT 28 T + 0.3938 0.3852 0.4697
LEUK_RAT 29 S +++ 0.6920 0.4029 0.4935
LEUK_RAT 33 S + 0.4933 0.4381 0.5409
LEUK_RAT 44 T +++ 0.6693 0.4165 0.5118
LEUK_RAT 50 S + 0.3897 0.3747 0.4554
LEUK_RAT 57 T ++ 0.5390 0.4111 0.5046
LEUK_RAT 58 T +++ 0.6271 0.4053 0.4967
LEUK_RAT 62 S + 0.4869 0.4238 0.5217
LEUK_RAT 63 S ++ 0.6100 0.4194 0.5157
LEUK_RAT 91 T + 0.4330 0.4060 0.4977
LEUK_RAT 92 T ++ 0.4961 0.3934 0.4807
LEUK_RAT 93 S + 0.4557 0.4124 0.5063
LEUK_RAT 97 S + 0.4692 0.4066 0.4985
LEUK_RAT 98 T + 0.5114 0.4222 0.5195
LEUK_RAT 108 S + 0.4984 0.4119 0.5056
LEUK_RAT 109 S +++ 0.6209 0.3978 0.4866
LEUK_RAT 118 T ++++ 0.7542 0.4267 0.5256
LEUK_RAT 120 T ++ 0.5358 0.4281 0.5274
LEUK_RAT 124 T +++ 0.6470 0.4087 0.5013
LEUK_RAT 125 S +++ 0.7343 0.4145 0.5091
LEUK_RAT 126 S ++ 0.6243 0.4313 0.5318
LEUK_RAT 131 T + 0.4973 0.4487 0.5552
LEUK_RAT 145 T ++++ 0.7629 0.4440 0.5489
LEUK_RAT 147 T +++ 0.6993 0.4525 0.5603
LEUK_RAT 148 S ++ 0.5850 0.4536 0.5618
LEUK_RAT 149 S + 0.5067 0.4533 0.5614
LEUK_RAT 153 S + 0.4848 0.4352 0.5370
LEUK_RAT 159 T ++ 0.6054 0.4765 0.5927
LEUK_RAT 162 S ++++ 0.7702 0.4242 0.5221
LEUK_RAT 163 S + 0.4354 0.4092 0.5019
LEUK_RAT 166 S + 0.4314 0.3751 0.4560
LEUK_RAT 171 T +++ 0.7201 0.4458 0.5513
LEUK_RAT 183 T + 0.4774 0.4040 0.4950
LEUK_RAT 192 T ++ 0.5797 0.4320 0.5327
LEUK_RAT 193 S +++ 0.6347 0.4159 0.5110
LEUK_RAT 194 S + 0.4443 0.3990 0.4883
LEUK_RAT 198 S + 0.4110 0.4073 0.4994
LEUK_RAT 208 S ++ 0.5823 0.4501 0.5571
LEUK_RAT 214 T + 0.4242 0.4092 0.5020
LEUK_RAT 221 T ++ 0.5461 0.4168 0.5122
LEUK_RAT 222 T ++ 0.6041 0.4159 0.5110
LEUK_RAT 229 S + 0.4820 0.4089 0.5016
LEUK_RAT 262 T ++ 0.4988 0.3886 0.4742
LEUK_RAT 292 T + 0.3937 0.3877 0.4730
LEUK_RAT 293 T ++ 0.5152 0.3967 0.4851
LEUK_RAT 295 S + 0.4397 0.3839 0.4678
LEUK_RAT 308 T ++ 0.5271 0.3720 0.4518
LEUK_RAT 318 T + 0.4814 0.4671 0.5800
LEUK_RAT 364 S ++ 0.5089 0.3646 0.4419
LEUK_RAT 377 S +++ 0.6489 0.3408 0.4097
----------------------------------------------------------
|
| Program name | Description |
|---|---|
| antigenic | Finds antigenic sites in proteins |
| digest | Reports on protein proteolytic enzyme or reagent cleavage sites |
| echlorop | Reports presence of chloroplast transit peptides |
| eiprscan | Motif detection |
| elipop | Prediction of lipoproteins |
| emast | Motif detection |
| ememe | Multiple EM for Motif Elicitation |
| ememetext | Multiple EM for Motif Elicitation. Text file only |
| 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 |
| epestfind | Finds PEST motifs as potential proteolytic cleavage sites |
| eprop | Reports propeptide cleavage sites in proteins |
| esignalp | Reports protein signal cleavage sites |
| etmhmm | Reports transmembrane helices |
| fuzzpro | Search for patterns in protein sequences |
| fuzztran | Search for patterns in protein sequences (translated) |
| helixturnhelix | Identify nucleic acid-binding motifs in protein sequences |
| oddcomp | Identify proteins with specified sequence word composition |
| omeme | Motif detection |
| patmatdb | Searches protein sequences with a sequence motif |
| patmatmotifs | Scan a protein sequence with motifs from the PROSITE database |
| pepcoil | Predicts coiled coil regions in protein sequences |
| preg | Regular expression search of protein sequence(s) |
| pscan | Scans protein sequence(s) with fingerprints from the PRINTS database |
| sigcleave | Reports on signal cleavage sites in a protein sequence |
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.