Details
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Type:
Improvement
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Status: Open
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Priority:
Critical
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Resolution: Unresolved
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Affects Version/s: None
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Fix Version/s: None
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Component/s: None
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Labels:None
Description
Infernal (used by Rfam, etc) annotates RNA structure to distinguish simple hairpins from other kinds of loops and stems. Although Jalview preserves these symbols in the annotation row, it could do more with them.
From Page 104 of Infernal's manual (http://eddylab.org/infernal/Userguide.pdf):
Full (output) WUSS notation
In detail, symbols used by WUSS notation in output structure annotation strings are as follows:
Base pairs
Base pairs are annotated by nested matching pairs of symbols <>, (), [], or {}. The different symbols indicate the “depth” of the helix in the RNA structure as follows: <> are used for simple terminal stems; () are used for “internal” helices enclosing a multifurcation of all terminal stems; [] are used for internal helices enclosing a multifurcation that includes at least one annotated () stem already; and {} are used for all internal helices enclosing deeper multifurcations.
Hairpin loops
Hairpin loop residues are indicated by underscores, _. Simple stem loops stand out as, e.g.
<<<<____>>>>.
Bulge, interior loops
Bulge and interior loop residues are indicated by dashes, -.
Multifurcation loops
Multifurcation loop residues are indicated by commas, ,. The mnemonic is “stem 1, stem2”, e.g.
<<<___>>>,,<<<___>>>.
External residues
Unstructured single stranded residues completely outside the structure (unenclosed by any base pairs) are annotated by colons, :.
Insertions
Insertions relative to a known structure are indicated by periods, .. Regions where local structural alignment was invoked, leaving regions of both target and query sequence unaligned, are indicated by tildes, ˜. These symbols only appear in alignments of a known (query) structure annotation to a target sequence of unknown structure.
Pseudoknots
WUSS notation allows pseudoknots to be annotated as pairs of upper case/lower case letters: for example, <<<<_AAAA____>>>>aaaa annotates a simple pseudoknot; additional pseudoknottedstems could be annotated by Bb, Cc, etc. Infernal cannot handle pseudoknots, however; pseudoknot notation never appears in Infernal output; it is accepted in input files, but ignored.
From Page 104 of Infernal's manual (http://eddylab.org/infernal/Userguide.pdf):
Full (output) WUSS notation
In detail, symbols used by WUSS notation in output structure annotation strings are as follows:
Base pairs
Base pairs are annotated by nested matching pairs of symbols <>, (), [], or {}. The different symbols indicate the “depth” of the helix in the RNA structure as follows: <> are used for simple terminal stems; () are used for “internal” helices enclosing a multifurcation of all terminal stems; [] are used for internal helices enclosing a multifurcation that includes at least one annotated () stem already; and {} are used for all internal helices enclosing deeper multifurcations.
Hairpin loops
Hairpin loop residues are indicated by underscores, _. Simple stem loops stand out as, e.g.
<<<<____>>>>.
Bulge, interior loops
Bulge and interior loop residues are indicated by dashes, -.
Multifurcation loops
Multifurcation loop residues are indicated by commas, ,. The mnemonic is “stem 1, stem2”, e.g.
<<<___>>>,,<<<___>>>.
External residues
Unstructured single stranded residues completely outside the structure (unenclosed by any base pairs) are annotated by colons, :.
Insertions
Insertions relative to a known structure are indicated by periods, .. Regions where local structural alignment was invoked, leaving regions of both target and query sequence unaligned, are indicated by tildes, ˜. These symbols only appear in alignments of a known (query) structure annotation to a target sequence of unknown structure.
Pseudoknots
WUSS notation allows pseudoknots to be annotated as pairs of upper case/lower case letters: for example, <<<<_AAAA____>>>>aaaa annotates a simple pseudoknot; additional pseudoknottedstems could be annotated by Bb, Cc, etc. Infernal cannot handle pseudoknots, however; pseudoknot notation never appears in Infernal output; it is accepted in input files, but ignored.