% edamhasoutput sequence 
Find EDAM ontology terms by has_output relation
Obo output file [edamhasoutput.obo]: 

Find EDAM ontology terms by has_output relation
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-identifier]        string     Identifier(s) to search for in ontology (Any
                                  string)
  [-outfile]           outobo     [*.edamhasoutput] 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: data (Data entity);
                                  entity (Biological entity); format (Data
                                  format); identifier (Identifier); operation
                                  (Bioinformatics operation); resource (Data
                                  resource); topic (Field of bioinformatics
                                  study))

   Advanced (Unprompted) qualifiers:
   -sensitive          boolean    [N] By default, the query keywords are
                                  matched against the EDAM term names (and
                                  synonyms) only. This option also matches the
                                  keywords against the EDAM term definitions
                                  and will therefore (typically) report more
                                  matches.
   -subclasses         boolean    [N] Extend the query matches to include all
                                  terms which are specialisations (EDAM
                                  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

[Term]
id: EDAM_operation:0290
name: Sequence redundancy removal
namespace: operation
def: Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria.
subset: bioinformatics
subset: edam
subset: operations
created_in: "beta12orEarlier"
is_a: EDAM_operation:0291 ! Sequence clustering
relationship: has_output EDAM_data:2044 ! Sequence
relationship: has_topic EDAM_topic:0164 ! Sequence clustering

[Term]
id: EDAM_operation:1813
name: Sequence retrieval
namespace: operation
def: Query a sequence data resource (typically a database) and retrieve sequences and / or annotation.
comment: This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence.
subset: bioinformatics
subset: edam
subset: operations
synonym: "Data retrieval (sequences)" EXACT []
created_in: "beta12orEarlier"
is_a: EDAM_operation:2422 ! Data retrieval
is_a: EDAM_operation:2446 ! Sequence processing
relationship: has_output EDAM_data:2044 ! Sequence

[Term]
id: EDAM_operation:2871
name: Sequence tagged site (STS) mapping
namespace: operation
def: Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS).
comment: An STS is a short subsequence of known sequence and location that occurs only once in the chromosome or genome that is being mapped. Sources of STSs include 1. expressed sequence tags (ESTs), simple sequence length polymorphisms (SSLPs), and random genomic sequences from cloned genomic DNA or database sequences.
subset: bioinformatics
subset: edam
subset: operations
synonym: "Sequence mapping" EXACT []
created_in: "beta12orEarlier"
is_a: EDAM_operation:2944 ! Physical mapping
relationship: has_output EDAM_data:1279 ! Sequence map

[Term]
id: EDAM_operation:0310
name: Sequence assembly
namespace: operation
def: Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence.
comment: For example, assemble overlapping reads from paired-end sequencers into contigs (a contiguous sequence corresponding to read overlaps). Or assemble contigs, for example ESTs and genomic DNA fragments, depending on the detected fragment overlaps.
subset: bioinformatics
subset: edam


  [Part of this file has been deleted for brevity]

subset: edam
subset: operations
created_in: "beta12orEarlier"
is_a: EDAM_operation:0337 ! Plotting and rendering
is_a: EDAM_operation:2463 ! Sequence alignment processing
relationship: has_input EDAM_data:0863 ! Sequence alignment
relationship: has_output EDAM_data:1711 ! Sequence alignment image

[Term]
id: EDAM_operation:0491
name: Pairwise sequence alignment construction
namespace: operation
def: Align exactly two molecular sequences.
comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons.
subset: bioinformatics
subset: edam
subset: operations
synonym: "Pairwise sequence alignment" EXACT []
created_in: "beta12orEarlier"
is_a: EDAM_operation:0292 ! Sequence alignment construction
relationship: has_output EDAM_data:1381 ! Sequence alignment (pair)

[Term]
id: EDAM_operation:0483
name: Structured RNA prediction and optimisation
namespace: operation
def: Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection.
subset: bioinformatics
subset: edam
subset: operations
synonym: "Nucleic acid folding family identification" EXACT []
synonym: "RNA inverse folding" EXACT []
created_in: "beta12orEarlier"
is_a: EDAM_operation:2425 ! Optimisation and refinement
is_a: EDAM_operation:3095 ! Nucleic acid design
relationship: has_output EDAM_data:1234 ! Sequence set (nucleic acid)
relationship: has_topic EDAM_topic:2953 ! Nucleic acid design

[Term]
id: EDAM_operation:0449
name: Sequence alignment analysis (site correlation)
namespace: operation
def: Analyse correlations between sites in a molecular sequence alignment.
comment: This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures.
subset: bioinformatics
subset: edam
subset: operations
created_in: "beta12orEarlier"
is_a: EDAM_operation:0258 ! Sequence alignment analysis
relationship: has_output EDAM_data:1416 ! Sequence alignment report (site correlation)