                                   goname



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Function

   Find GO ontology terms by name

Description

   goname searches the names and synonyms of gene ontology terms and
   returns matching terms. The input is read from the installed GO
   database. The ontology term output can be written to screen, to file,
   or passed to another program. A wide range of standard ontology term
   formats may be specified for input and output.

   Optionally the search can be restricted to specified GO namespaces.

Usage

   Here is a sample session with goname


% goname glycoprotein
Find GO ontology terms by name
Obo output file [goname.obo]:


   Go to the output files for this example

Command line arguments

Find GO ontology terms by name
Version: EMBOSS:6.5.6.0

   Standard (Mandatory) qualifiers:
  [-query]             string     Name(s) to search for in ontology (Any
                                  string)
  [-outfile]           outobo     [*.goname] Output ontology term file name

   Additional (Optional) qualifiers:
   -namespace          menu       [*] By default all terms are returned.
                                  Searches can be limited to one or a few
                                  namespaces. (Values: biological_process
                                  (Biological process); cellular_component
                                  (Cellular component); molecular_function
                                  (Molecular function))

   Advanced (Unprompted) qualifiers:
   -subclasses         boolean    [N] Extend the query matches to include all
                                  terms which are specialisations (GO
                                  sub-classes) of the matched type.
   -obsolete           boolean    [N] The default behaviour is to not use or
                                  return obsolete terms. This option if set
                                  will include all terms.

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory
   -oformat2           string     Ontology term output format

   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

   goname queries the gene ontology.

Output file format

   The output is a standard EMBOSS ontology term file.

   The results can be output in one of several styles by using the
   command-line qualifier -oformat xxx, where 'xxx' is replaced by the
   name of the required format. The available format names are: obo,
   brief, list, html, xml, json, excel.

   See: http://emboss.sf.net/docs/themes/OntologyFormats.html for further
   information on ontology formats.

  Output files for usage example

  File: goname.obo

[Term]
id: GO:0036071
name: N-glycan fucosylation
namespace: biological_process
def: The process of transferring a fucosyl group to an N-glycan. An N-glycan is
the carbohydrate portion of an N-glycoprotein when attached to a nitrogen from a
sparagine or arginine side-chains.
synonym: "glycoprotein fucosylation" RELATED [GOC:bf]
is_a: GO:0036065 ! fucosylation

[Term]
id: GO:0035977
name: protein deglycosylation involved in glycoprotein catabolic process
namespace: biological_process
def: The removal of sugar residues from a glycosylated protein that contributes
to the breakdown of a glycoprotein.
is_a: GO:0006517 ! protein deglycosylation
relationship: part_of GO:0006516 ! glycoprotein catabolic process

[Term]
id: GO:0034436
name: glycoprotein transport
namespace: biological_process
def: The directed movement of a glycoprotein, any protein that contains covalent
ly bound glycose (i.e. monosaccharide) residues, into, out of or within a cell,
or between cells, by means of some agent such as a transporter or pore.
is_a: GO:0015031 ! protein transport

[Term]
id: GO:0008424
name: glycoprotein 6-alpha-L-fucosyltransferase activity
namespace: molecular_function
def: Catalysis of the reaction: N(4)-{N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-
D-mannosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->6)]-
beta-D-mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-N-acetyl-beta-D-gluco
saminyl}-L-asparagine + GDP-L-fucose = N(4)-{N-acetyl-beta-D-glucosaminyl-(1->2)
-alpha-D-mannosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(
1->6)]-beta-D-mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-[alpha-L-fucos
yl-(1->6)]-N-acetyl-beta-D-glucosaminyl}asparagine + GDP + H(+).
synonym: "FucT" RELATED [EC:2.4.1.68]
synonym: "GDP-fucose--glycoprotein fucosyltransferase activity" EXACT [EC:2.4.1.
68]
synonym: "GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha(1,6)fucosyltransferase a
ctivity" EXACT [EC:2.4.1.68]
synonym: "GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha(1->6)fucosyltransferase
activity" EXACT [EC:2.4.1.68]
synonym: "GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha-(1,6)fucosyltransferase
activity" EXACT [EC:2.4.1.68]
synonym: "GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha-(1->6)fucosyltransferase
 activity" EXACT [EC:2.4.1.68]
synonym: "GDP-L-fucose--glycoprotein fucosyltransferase activity" EXACT [EC:2.4.
1.68]
synonym: "GDPfucose-glycoprotein fucosyltransferase activity" EXACT [EC:2.4.1.68
]
synonym: "glycoprotein fucosyltransferase activity" BROAD [EC:2.4.1.68]
synonym: "guanosine diphosphofucose--glycoprotein fucosyltransferase activity" E
XACT [EC:2.4.1.68]
xref: EC:2.4.1.68
xref: KEGG:R05988
xref: MetaCyc:2.4.1.68-RXN
xref: Reactome:REACT_25399 "Addition of alpha 1,6 fucose to the first GlcNAc of
the N-glycan, Homo sapiens"
xref: RHEA:12988
is_a: GO:0046921 ! alpha-(1->6)-fucosyltransferase activity

[Term]
id: GO:0018010
name: glycoprotein N-palmitoyltransferase activity
namespace: molecular_function
def: Catalysis of the reaction: palmitoyl-CoA + glycoprotein = CoA + N-palmitoyl
glycoprotein.


  [Part of this file has been deleted for brevity]

synonym: "cell wall hydroxyproline-rich glycoprotein metabolism" EXACT []
is_a: GO:0010384 ! cell wall proteoglycan metabolic process

[Term]
id: GO:0004653
name: polypeptide N-acetylgalactosaminyltransferase activity
namespace: molecular_function
def: Catalysis of the reaction: UDP-N-acetyl-D-galactosamine + polypeptide = UDP
 + N-acetyl-D-galactosaminyl-polypeptide. This reaction is the modification of s
erine or threonine residues in polypeptide chains by the transfer of a N-acetylg
alactose from UDP-N-acetylgalactose to the hydroxyl group of the amino acid; it
is the first step in O-glycan biosynthesis.
synonym: "glycoprotein acetylgalactosaminyltransferase activity" EXACT [EC:2.4.1
.41]
synonym: "polypeptide-N-acetylgalactosamine transferase activity" EXACT [EC:2.4.
1.41]
synonym: "protein-UDP acetylgalactosaminyltransferase activity" EXACT [EC:2.4.1.
41]
synonym: "UDP-acetylgalactosamine-glycoprotein acetylgalactosaminyltransferase a
ctivity" EXACT [EC:2.4.1.41]
synonym: "UDP-acetylgalactosamine:peptide-N-galactosaminyltransferase activity"
EXACT [EC:2.4.1.41]
synonym: "UDP-GalNAc:polypeptide N-acetylgalactosaminyl transferase activity" EX
ACT [EC:2.4.1.41]
synonym: "UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase activity" EXA
CT [EC:2.4.1.41]
synonym: "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminylt
ransferase activity" EXACT [EC:2.4.1.41]
synonym: "UDP-N-acetyl-D-galactosamine:polypeptide N-acetylgalactosaminyl-transf
erase activity" EXACT [EC:2.4.1.41]
synonym: "UDP-N-acetylgalactosamine-glycoprotein N-acetylgalactosaminyltransfera
se activity" EXACT [EC:2.4.1.41]
synonym: "UDP-N-acetylgalactosamine-protein N-acetylgalactosaminyltransferase ac
tivity" EXACT [EC:2.4.1.41]
synonym: "UDP-N-acetylgalactosamine:kappa-casein polypeptide N-acetylgalactosami
nyltransferase activity" EXACT [EC:2.4.1.41]
synonym: "UDP-N-acetylgalactosamine:polypeptide N-acetylgalactosaminyltransferas
e activity" EXACT [EC:2.4.1.41]
synonym: "UDP-N-acetylgalactosamine:protein N-acetylgalactosaminyl transferase a
ctivity" EXACT [EC:2.4.1.41]
synonym: "uridine diphosphoacetylgalactosamine-glycoprotein acetylgalactosaminyl
transferase activity" EXACT [EC:2.4.1.41]
xref: EC:2.4.1.41
xref: MetaCyc:2.4.1.41-RXN
xref: Reactome:REACT_115586 "Addition of GalNAc to mucins to form the Tn antigen
, Homo sapiens"
is_a: GO:0008376 ! acetylgalactosaminyltransferase activity

[Term]
id: GO:0003827
name: alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase acti
vity
namespace: molecular_function
def: Catalysis of the reaction: 3-(alpha-D-mannosyl)-beta-D-mannosyl-R + UDP-N-a
cetyl-alpha-D-glucosamine = 3-(2-[N-acetyl-beta-D-glucosaminyl]-alpha-D-mannosyl
)-beta-D-mannosyl-R + H(+) + UDP.
synonym: "alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
 activity" EXACT [EC:2.4.1.101]
synonym: "alpha-1,3-mannosyl-glycoprotein beta-1,2-N-acetylglucosaminyltransfera
se activity" EXACT [EC:2.4.1.101]
synonym: "alpha-1,3-mannosylglycoprotein beta-1,2-N-acetylglucosaminyltransferas
e activity" EXACT []
synonym: "GnTI" RELATED [EC:2.4.1.101]
synonym: "GNTI activity" EXACT [EC:2.4.1.101]
synonym: "N-acetylglucosaminyltransferase I activity" EXACT [EC:2.4.1.101]
synonym: "N-glycosyl-oligosaccharide-glycoprotein N-acetylglucosaminyltransferas
e I activity" EXACT [EC:2.4.1.101]
synonym: "UDP-N-acetyl-D-glucosamine:3-(alpha-D-mannosyl)-beta-D-mannosyl-glycop
rotein 2-beta-N-acetyl-D-glucosaminyltransferase activity" EXACT [EC:2.4.1.101]
synonym: "UDP-N-acetylglucosaminyl:alpha-1,3-D-mannoside-beta-1,2-N-acetylglucos
aminyltransferase I activity" EXACT [EC:2.4.1.101]
synonym: "UDP-N-acetylglucosaminyl:alpha-3-D-mannoside beta-1,2-N-acetylglucosam
inyltransferase I activity" EXACT [EC:2.4.1.101]
synonym: "uridine diphosphoacetylglucosamine-alpha-1,3-mannosylglycoprotein beta
-1,2-N-acetylglucosaminyltransferase activity" EXACT [EC:2.4.1.101]
xref: EC:2.4.1.101
xref: KEGG:R05983
xref: MetaCyc:2.4.1.101-RXN
xref: Reactome:REACT_25236 "Addition of GlcNAc to the glycan on the A arm, Homo
sapiens"
xref: RHEA:11459
is_a: GO:0008375 ! acetylglucosaminyltransferase activity


Data files

   The gene Ontology is included in EMBOSS as local database go.

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
                    edamdef         Find EDAM ontology terms by definition
                    edamhasinput    Find EDAM ontology terms by has_input relation
                    edamhasoutput   Find EDAM ontology terms by has_output relation
                    edamisformat    Find EDAM ontology terms by is_format_of relation
                    edamisid        Find EDAM ontology terms by is_identifier_of relation
                    edamname        Find EDAM ontology terms by name
                    godef           Find GO ontology terms by definition
                    ontoget         Get ontology term(s)
                    ontogetcommon   Get common ancestor for terms
                    ontogetdown     Get ontology term(s) by parent id
   ontogetobsolete  Get ontology ontology terms
                    ontogetroot     Get ontology root terms by child identifier
                    ontogetsibs     Get ontology term(s) by id with common parent
                    ontogetup       Get ontology term(s) by id of child
                    ontoisobsolete  Report whether an ontology term id is obsolete
                    ontotext        Get ontology term(s) original full text

Author(s)

   Peter            Rice
   European         Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton,         Cambridge CB10 1SD, UK

                    Please report all bugs to the EMBOSS bug team
                    (emboss-bug (c) 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
