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Fix #16 and add internal links (#24)

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Juke34 authored and alexhenrie committed Nov 12, 2019
1 parent b420af0 commit 31f62ad469b31769b43af42e0903448db1826925
Showing with 5 additions and 5 deletions.
  1. +5 −5 gff3.md
10 gff3.md
@@ -72,19 +72,19 @@ Undefined fields are replaced with the "." character, as described in the origin
<dd>Display name for the feature. This is the name to be displayed to the user. Unlike IDs, there is no requirement that the Name be unique within the file.</dd>
<dt>Alias</dt>
<dd>A secondary name for the feature. It is suggested that this tag be used whenever a secondary identifier for the feature is needed, such as locus names and accession numbers. Unlike ID, there is no requirement that Alias be unique within the file.</dd>
<dt>Parent</dt>
<dt><a href="#parent-part_of-relationships">Parent</a></dt>
<dd>Indicates the parent of the feature. A parent ID can be used to group exons into transcripts, transcripts into genes, an so forth. A feature may have multiple parents. Parent can <em>only</em> be used to indicate a partof relationship.</dd>
<dt>Target</dt>
<dd>Indicates the target of a nucleotide-to-nucleotide or protein-to-nucleotide alignment. The format of the value is "target_id start end [strand]", where strand is optional and may be "+" or "-". If the target_id contains spaces, they must be escaped as hex escape %20.</dd>
<dt>Gap</dt>
<dd>The alignment of the feature to the target if the two are not collinear (e.g. contain gaps). The alignment format is taken from the CIGAR format described in the <a href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/exonerate/?root=ensembl">Exonerate documentation</a>. See "THE GAP ATTRIBUTE" for a description of this format.</dd>
<dt><a href="#the-gap-attribute">Gap</a></dt>
<dd>The alignment of the feature to the target if the two are not collinear (e.g. contain gaps). The alignment format is inspired from the CIGAR format described in the <a href="https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate-manual">Exonerate documentation</a>.</dd>
<dt>Derives_from</dt>
<dd>Used to disambiguate the relationship between one feature and another when the relationship is a temporal one rather than a purely structural "part of" one. This is needed for polycistronic genes. See "PATHOLOGICAL CASES" for further discussion.</dd>
<dt>Note</dt>
<dd>A free text note.</dd>
<dt>Dbxref</dt>
<dt><a href="#ontology-associations-and-db-cross-references">Dbxref</a></dt>
<dd>A database cross reference. See the section "Ontology Associations and Db Cross References" for details on the format.</dd>
<dt>Ontology_term</dt>
<dt><a href="#ontology-associations-and-db-cross-references">Ontology_term</a></dt>
<dd>A cross reference to an ontology term. See the section "Ontology Associations and Db Cross References" for details.</dd>
<dt>Is_circular</dt>
<dd>A flag to indicate whether a feature is circular. See extended discussion below.</dd>

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