<commit_before><html>
<head>
<title>Annotation of Non-Coding RNA</title>
</head>

<body>

<h1>Non-coding RNA Overview</h1>

<p>
The majority of non-coding RNA, or ncRNA, in Ensembl has been generated using RFAM.  
A small handpicked set is also available.  This
<a href="ftp://ftp.genetics.wustl.edu/pub/eddy/annotation/human-hg16/" rel="external">ncRNA set</a>, 
as well as a detailed
<a href="ftp://ftp.genetics.wustl.edu/pub/eddy/annotation/human-chr2+4/methods-hg16_chr2+4" rel="external">description</a> 
of the annotation methods can be obtained from
<a href="ftp://ftp.genetics.wustl.edu/" rel="external">ftp.genetics.wustl.edu</a>.
</p>

<p>
The following non-coding RNA gene types are annotated, along with pseudogenes
</p>

<dl>

<dt>tRNA</dt><dd>nuclear transfer RNA</dd>
<dt>Mt-tRNA</dt><dd>mitochondrially-derived tRNA located in the nuclear genome</dd>
<dt>rRNA</dt><dd>ribosomal RNA</dd>
<dt>scRNA</dt><dd>small cytoplasmic RNA</dd>
<dt>snRNA</dt><dd>small nuclear RNA</dd> 
<dt>snoRNA</dt><dd>small nucleolar RNA</dd> 
<dt>miRNA</dt><dd>microRNA precursors</dd> 
<dt>misc_RNA</dt><dd>miscellaneous other RNA</dd>

</dl>

<h2 id="Details">Annotation Details</h2>

<p>
Most <strong>ncRNA</strong> is annotated by aligning genomic sequence against 
<a rel="external" href="http://rfam.sanger.ac.uk/">RFAM</a> using 
<a rel="external" href="http://blast.wustl.edu/">BLASTN</a>. 
The BLAST hits are clustered and filtered by E value and are used to seed Infernal 
searches of the locus with the corresponding RFAM covariance models. The purpose of 
this is to reduce the search space required, as to scan the entire genome with all 
the RFAM covariance models would be extremely CPU-intensive. The resulting BLAST hits 
are then used as supporting evidence for ncRNA genes.
</p>
<p>
<strong>miRNA</strong> is predicted by BLASTN of genomic sequence slices against 
<a rel="external" href="http://microrna.sanger.ac.uk/">miRBase</a> sequences. 
The BLAST hits are clustered and filtered by E value and the aligned genomic sequence 
is then checked for possible secondary structure using RNAFold. If evidence is found 
that the genomic sequence could form a stable hairpin structure, the locus is used to 
create a miRNA gene model. The resulting BLAST hit is used as supporting evidence for the miRNA gene. 
</p>

</body>
</html><commit_msg>Removed references to Sean Eddy's hand checked set and corrected Mt-tRNAs.<commit_after><html>
<head>
<title>Annotation of Non-Coding RNAs</title>
</head>

<body>

<h1>Annotation of Non-Coding RNAs</h1>

<h2>Non-coding RNA Overview</h2>

<p>
<strong>Non-coding RNAs</strong> (ncRNAs) are involved in many
biological processes and are increasingly seen as important. As is the
case with proteins, it is the overall structure of the molecule which
imparts function. However, while similar protein structures are often
reflected in a conserved amino acid sequence, sequences underlying RNA
secondary structure are very variable; this makes ncRNAs difficult to
detect using sequence alone.
</p>

<p>
Because of this, we use a variety of techniques to detect
ncRNAs. First, a combination of sensitive BLAST searches are used to
identify likely targets, then a covariance model search is used to
measure the probability that the targets can fold into the structures
required. Other ncRNAs are added as part of the raw compute stage.
</p>

<p>
The following non-coding RNA gene types are annotated, along with pseudogenes
</p>

<dl>

<dt>tRNA</dt><dd>transfer RNA</dd>
<dt>Mt-tRNA</dt><dd>transfer RNA located in the mitochondrial genome</dd>
<dt>rRNA</dt><dd>ribosomal RNA</dd>
<dt>scRNA</dt><dd>small cytoplasmic RNA</dd>
<dt>snRNA</dt><dd>small nuclear RNA</dd> 
<dt>snoRNA</dt><dd>small nucleolar RNA</dd> 
<dt>miRNA</dt><dd>microRNA precursors</dd> 
<dt>misc_RNA</dt><dd>miscellaneous other RNA</dd>

</dl>

<h2 id="Details">Annotation Details</h2>

<p>
Most <strong>ncRNAs</strong> are annotated by aligning genomic
sequence against <a rel="external"
href="http://rfam.sanger.ac.uk/">RFAM</a> using <a rel="external"
href="http://blast.wustl.edu/">BLASTN</a>. The BLAST hits are
clustered and filtered by E value and are used to seed Infernal
searches of the locus with the corresponding RFAM covariance
models. The purpose of this is to reduce the search space required, as
to scan the entire genome with all the RFAM covariance models would be
extremely CPU-intensive. The resulting BLAST hits are then used as
supporting evidence for ncRNA genes.
</p>

<p>
<strong>miRNAs</strong> are predicted by BLASTN of genomic sequence
slices against <a rel="external"
href="http://microrna.sanger.ac.uk/">miRBase</a> sequences. The BLAST
hits are clustered and filtered by E value and the aligned genomic
sequence is then checked for possible secondary structure using
RNAFold. If evidence is found that the genomic sequence could form a
stable hairpin structure, the locus is used to create a miRNA gene
model. The resulting BLAST hit is used as supporting evidence for the
miRNA gene.
</p>

<p>
<strong>tRNAs</strong> are annotated as part of the raw compute
process using <a rel="external"
href="http://lowelab.ucsc.edu/tRNAscan-SE/">tRNAscan-SE</a>.
</p>

</body>
</html>
{'fraction_non_alphanumeric': 0.11192027596780375, 'fraction_numerical': 0.0034495975469528554, 'mean_word_length': 4.991963260619977, 'pattern_counts': {'":': 0, '<': 149, '<?xml version=': 0, '>': 149, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4930075', 'n_tokens_mistral': 1813, 'n_tokens_neox': 1605, 'n_words': 634}