                                  eyinoyang



Wiki

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Function

   Reports O-(beta)-GlcNAc attachment sites

Description

   The YinOYang WWW server produces neural network predictions for
   O-ss-GlcNAc attachment sites in eukaryotic protein sequences. This
   server can also use NetPhos, to mark possible phosphorylated sites and
   hence identify "Yin-Yang" sites.

Usage

   Here is a sample session with eyinoyang


% eyinoyang
Reports O-(beta)-GlcNAc attachment sites
Input (aligned) sequence set: CBG_HUMAN.fsa
Output file [cbg_human.eyinoyang]:


   Go to the input files for this example
   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

Command line arguments

Reports O-(beta)-GlcNAc attachment sites
Version: EMBOSS:6.2.0

   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


Input file format

   eyinoyang reads any normal sequence USAs.

  Input files for usage example

  File: CBG_HUMAN.fsa

>CBG_HUMAN
MPLLLYTCLLWLPTSGLWTVQAMDPNAAYVNMSNHHRGLASANVDFAFSLYKHLVALSPK
KNIFISPVSISMALAMLSLGTCGHTRAQLLQGLGFNLTERSETEIHQGFQHLHQLFAKSD
TSLEMTMGNALFLDGSLELLESFSADIKHYYESEVLAMNFQDWATASRQINSYVKNKTQG
KIVDLFSGLDSPAILVLVNYIFFKGTWTQPFDLASTREENFYVDETTVVKVPMMLQSSTI
SYLHDSELPCQLVQMNYVGNGTVFFILPDKGKMNTVIAALSRDTINRWSAGLTSSQVDLY
IPKVTISGVYDLGDVLEEMGIADLFTNQANFSRITQDAQLKSSKVVHKAVLQLNEEGVDT
AGSTGVTLNLTSKPIILRFNQPFIIMIFDHFTWSSLFLARVMNPV

  Input files for usage example 2

  File: LEUK_RAT.fsa

>LEUK_RAT P13838 LEUKOSIALIN PRECURSOR (LEUCOCYTE SIALOGLYCOPROTEIN) (SIALOPHORI
N) (CD43) (W3/13 ANTIGEN) (FRAGMENT). - RATTUS NORVEGICUS (RAT).
WAQVVSQENLPNTMTMLPFTPNSESPSTSEALSTYSSIATVPVTEDPKESISPWGQTTAP
ASSIPLGTPELSSFFFTSAGASGNTPVPELTTSQEVSTEASLVLFPKSSGVASDPPVTIT
NPATSSAVASTSLETFKGTSAPPVTVTSSTMTSGPFVATTVSSETSGPPVTMATGSLGPS
KETHGLSATIATSSGESSSVAGGTPVFSTKISTTSTPNPITTVPPRPGSSGMLLVSMLIA
LTVVLVLVALLLLWRQRQKRRTGALTLSRGGKRNGTVDAWAGPARVPDEEATTASGSGGN
KSSGAPETDGSGQRPTLTTFFSRRKSRQGSVALEELKPGTGPNLKGEEEPLVGSEDEAVE
TPTSDGPQAKDGAAPQSL

Output file format

  Output files for usage example

  File: cbg_human.eyinoyang

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
----------------------------------------------------------

  Output files for usage example 2

  File: leuk_rat.eyinoyang

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
----------------------------------------------------------

Data files

   None.

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   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

Author(s)

   This program is an EMBOSS wrapper for a program written by the CBS
   group http://www.cbs.dtu.dk/index.shtml

   The original CBS group application must be licensed and installed to
   use this wrapper.

   Although we take every care to ensure that the results of the EMBOSS
   version are identical to those from the original package, we recommend
   that you check your inputs give the same results in both versions
   before publication.

   Please report all bugs in the EMBOSS version to the EMBOSS bug team,
   not to the original author.

History

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
