enetnglyc

 

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Function

Report 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 
Report N-glycosylation sites in human proteins
Input (aligned) protein 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

Report N-glycosylation sites in human proteins
Version: EMBOSS:6.5.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     (Aligned) protein 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
   -scircular1         boolean    Sequence is circular
   -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 <*>.enetnglyc
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-plot boolean Produce graphics Boolean value Yes/No No
-asparagines boolean Predict on all asparagines Boolean value Yes/No No
-thresholds boolean Show additional thresholds when -plot is used 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
-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

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) (SIALOPHORIN) (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
enetoglyc Reports mucin type GalNAc O-glycosylation sites in mammalian 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

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.

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) 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