Commit 880d186c authored by Blake Sweeney's avatar Blake Sweeney
Browse files

Update links to point to QC pages

This now has a generic QC page and all previous rfam-annotations link
point to it. It is a generic QC page since we now also use CPAT to
annotate.
parent 8a9901d7
......@@ -92,7 +92,7 @@ class Command(BaseCommand):
'help-gene-ontology-annotations',
'help-genomic-mapping',
'help-public-database',
'help-rfam-annotations',
'help-qc',
'help-rna-target-interactions',
'help-scientific-advisory-board',
'help-secondary-structure',
......
......@@ -128,7 +128,7 @@ class DomainProblem(object):
match_domain=model.domain,
model_url=model.url,
model_name=model.short_name,
help_url=reverse('help-rfam-annotations'),
help_url=reverse('help-qc'),
)
)
......
......@@ -47,7 +47,7 @@ var sequenceSearchController = function($scope, $http, $timeout, $location, $q,
};
$scope.help = {
rfam: "/help/rfam-annotations",
rfam: "/help/qc",
crs: "/help/conserved-motifs",
go: "/help/gene-ontology-annotations",
genomeMapping: "/help/genomic-mapping"
......
......@@ -10,7 +10,7 @@ var rfam = {
var ctrl = this;
ctrl.$onInit = function() {
ctrl.help = "/help/rfam-annotations";
ctrl.help = "/help/qc";
// group hits with same rfam_model_id
ctrl.groupedHits = [];
......
......@@ -6,6 +6,6 @@
<p ng-if="warning === 'missing_match'">This sequence does not match the expected Rfam family</p>
</span>
<p>
<a href="/help/rfam-annotations" style="color: #fff">Learn more &rarr;</a>
<a href="/help/qc" style="color: #fff">Learn more &rarr;</a>
</p>
</div>
## What is Rfam?
[Rfam](http://rfam.org) is a database of functional non-coding RNA families represented by multiple sequence alignments and consensus secondary structures. The sequence and structural information is used to build [Infernal](http://eddylab.org/infernal/) covariance models, which can be used to find new instances of RNA families and annotate genomes with non-coding RNAs.
RNAcentral provides a variety of quality checks for all sequences. Many of these checks are based off of [Rfam](http://rfam.org). [Rfam](http://rfam.org) is a database of functional non-coding RNA families represented by multiple sequence alignments and consensus secondary structures. The sequence and structural information is used to build [Infernal](http://eddylab.org/infernal/) covariance models, which can be used to find new instances of RNA families and annotate genomes with non-coding RNAs.
Every release RNAcentral annotates **all sequences** with Rfam models. Rfam classification provides additional context to sequences with few annotations and help identify **potential problems**, for example, sequences which are likely contamination.
## Three types of quality control using Rfam
In addition to Rfam based checks we also use [CPAT](https://academic.oup.com/nar/article/41/6/e74/2902455) to analyze sequences. This tool detects possible open reading frames in sequences. We analyze **all** human, fly, mouse and zebrafish sequences this way. We use CPAT version 3.0.4 with the default options.
## Current types of quality control
### 1. Incomplete sequences
......@@ -43,6 +43,17 @@ The majority of RNAcentral sequences annotated as rRNA or tRNA match the corresp
Browse all sequences with missing matches by searching for [`qc_warning:"missing_rfam_match"`](/search?q=qc_warning:%22missing_rfam_match%22).
### 4. Possible ORFs
Very few sequences contain open reading frames, however, it is worth noting which do as this may the function of the ncRNA.
#### Examples
* [Human lncRNA](/rna/URS00008D8914/9606)
* [Fly rRNA](/rna/URS0000745350/7227)
* [All sequences with ORFs](/search?q=qc_warning:%22possible_orf%22)
## Why some sequences do not match any Rfam families
There are several possible reasons:
......
......@@ -28,16 +28,16 @@ Help: Rfam annotations
<div class="row">
<div class="col-md-8" role="main">
<h1><i class="fa fa-map-marker"></i> Rfam annotations</h1>
<h1><i class="fa fa-map-marker"></i> Quality Control</h1>
{% load markdown_deux_tags %}
{% markdown %}
{% include 'portal/docs/rfam-annotations.md' %}
{% include 'portal/docs/qc.md' %}
{% endmarkdown %}
<hr>
<a class="btn btn-default btn-sm" title="Edit on GitHub" href="https://github.com/RNAcentral/rnacentral-webcode/edit/master/rnacentral/portal/templates/portal/docs/rfam-annotations.md" target="_blank"><i class="fa fa-pencil-square-o"></i> Improve this page</a>
<a class="btn btn-default btn-sm" title="Edit on GitHub" href="https://github.com/RNAcentral/rnacentral-webcode/edit/master/rnacentral/portal/templates/portal/docs/qc.md" target="_blank"><i class="fa fa-pencil-square-o"></i> Improve this page</a>
</div>
<div class="col-md-4">
......
......@@ -19,7 +19,7 @@
<strong>Functional annotations</strong>
<li><a href="{% url 'help-genomic-mapping' %}">Genomic mapping</a></li>
<li><a href="{% url 'help-secondary-structure' %}">Secondary structure <span class="label label-success">New<span></a></li>
<li><a href="{% url 'help-rfam-annotations' %}">Rfam annotations</a></li>
<li><a href="{% url 'help-qc' %}">QC annotations</a></li>
<li><a href="{% url 'help-gene-ontology-annotations' %}">Gene Ontology annotations</a></li>
<li><a href="{% url 'help-rna-target-interactions' %}">RNA-target interactions</a></li>
<li><a href="{% url 'help-conserved-motifs' %}">Conserved RNA motifs</a></li>
......
......@@ -127,7 +127,7 @@ class PortalTest(TestCase):
self.assertEqual(response.status_code, 200)
def test_help_rfam_annotations_status_code(self):
response = self.client.get(reverse('help-rfam-annotations'))
response = self.client.get(reverse('help-qc'))
self.assertEqual(response.status_code, 200)
def test_help_rna_target_interactions_status_code(self):
......
......@@ -46,7 +46,7 @@ urlpatterns = [
url(r'^help/?$', views.StaticView.as_view(), {'page': 'help/faq'}, name='help'),
url(r'^help/browser-compatibility/?$', views.StaticView.as_view(), {'page': 'help/browser-compatibility'}, name='help-browser-compatibility'),
url(r'^help/text-search/?$', views.StaticView.as_view(), {'page': 'help/text-search'}, name='help-text-search'),
url(r'^help/rfam-annotations/?$', views.StaticView.as_view(), {'page': 'help/rfam-annotations'}, name='help-rfam-annotations'),
url(r'^help/qc/?$', views.StaticView.as_view(), {'page': 'help/qc'}, name='help-qc'),
url(r'^help/rna-target-interactions/?$', views.StaticView.as_view(), {'page': 'help/rna-target-interactions'}, name='help-rna-target-interactions'),
url(r'^help/gene-ontology-annotations/?$', views.StaticView.as_view(), {'page': 'help/gene-ontology-annotations'}, name='help-gene-ontology-annotations'),
url(r'^help/genomic-mapping/?$', views.StaticView.as_view(), {'page': 'help/genomic-mapping', 'assemblies': EnsemblAssembly.objects.filter(example_chromosome__isnull=False).all()}, name='help-genomic-mapping'),
......
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