                                  enetnglyc



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Function

   Reports N-glycosylation sites in human proteins

Description

   The NetNglyc server predicts N-Glycosylation sites in human proteins
   using artificial neural networks that examine the sequence context of
   Asn-Xaa-Ser/Thr sequons.

Usage

   Here is a sample session with enetnglyc


% enetnglyc
Reports N-glycosylation sites in human proteins
Input (aligned) sequence set: LEUK_RAT.fsa
Output file [leuk_rat.enetnglyc]:


   Go to the input files for this example
   Go to the output files for this example

Command line arguments

Reports N-glycosylation sites in human proteins
Version: EMBOSS:6.2.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     (Aligned) sequence set filename and optional
                                  format, or reference (input USA)
  [-outfile]           outfile    [*.enetnglyc] Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -plot               boolean    [N] Produce graphics
   -asparagines        boolean    [N] Predict on all asparagines
   -thresholds         boolean    [N] Show additional thresholds when -plot is
                                  used

   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

   enetnglyc reads any normal sequence USAs.

  Input files for usage example

  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: leuk_rat.enetnglyc

# Predictions for N-Glycosylation sites in 1 sequence

################################################################################
########

    Warning: This sequence may not contain a signal peptide!!

    Proteins without signal peptides are unlikely to be exposed to
    the N-glycosylation machinery and thus may not be glycosylated
    (in vivo) even though they contain potential motifs.

    SignalP-NN euk predictions are as follows:

  # name                Cmax  pos ?  Ymax  pos ?  Smax  pos ?  Smean ?  D     ?
  LEUK_RAT              0.112  32 N  0.088  16 N  0.362   8 N  0.119 N  0.104 N

    SignalP output is explained at http://www.cbs.dtu.dk/services/SignalP/output
.html

################################################################################
########

Name:  LEUK_RAT         Length:  378
WAQVVSQENLPNTMTMLPFTPNSESPSTSEALSTYSSIATVPVTEDPKESISPWGQTTAPASSIPLGTPELSSFFFTSAG
      80
ASGNTPVPELTTSQEVSTEASLVLFPKSSGVASDPPVTITNPATSSAVASTSLETFKGTSAPPVTVTSSTMTSGPFVATT
     160
VSSETSGPPVTMATGSLGPSKETHGLSATIATSSGESSSVAGGTPVFSTKISTTSTPNPITTVPPRPGSSGMLLVSMLIA
     240
LTVVLVLVALLLLWRQRQKRRTGALTLSRGGKRNGTVDAWAGPARVPDEEATTASGSGGNKSSGAPETDGSGQRPTLTTF
     320
FSRRKSRQGSVALEELKPGTGPNLKGEEEPLVGSEDEAVETPTSDGPQAKDGAAPQSL
     400
................................................................................
      80
................................................................................
     160
................................................................................
     240
.................................N.........................N....................
     320
..........................................................
     400

(Threshold=0.5)
----------------------------------------------------------------------
SeqName        Position      Potential          Jury          N-Glyc
                                              agreement       result
----------------------------------------------------------------------
LEUK_RAT       274 NGTV         0.7323          (9/9)             ++
LEUK_RAT       300 NKSS         0.5404          (6/9)              +
----------------------------------------------------------------------


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
   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
   eyinoyang        Reports O-(beta)-GlcNAc attachment sites
   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
