<commit_before><html>
<head>
<title>Core databases and API</title>
</head>

<body>

<h1>Ensembl Core and OtherFeatures databases</h1>


<h2>Database Descriptions</h2>


<h3>Core database</h3>

<p>
For each organism supported by Ensembl, a species-specific Ensembl
Core database stores the bulk of annotation information.  Some of the
key features are:
</p>

<ul>
<li>
The unmasked genome sequence is stored on the sequence-level i.e. in
form of BAC clones or whole genome shotgun scaffolds.
</li>

<li>
Assembly information the generate top-level sequences like chromosomes
from sequence-level entities.
</li>

<li>
The non-redundant set of Ensembl gene, transcript and protein models
annotated by the automated genome analysis and
<a href="/info/docs/genebuild/genome_annotation.html">annotation
pipeline</a>.
</li>

<li>
Sequence tagged sites (STS) marker information on physical sequence
and genetic map locations.
</li>

<li>
Cytogenetic banding patterns if a reliable banding pattern has been
established for the organism.
</li>

<li>
Microarray probe set annotation.
</li>

<li>
External references to other databases of biological information.
</li>

<li>
cDNA and protein alignments supporting the transcript models that have
been built. The cDNA alignments found in the core database are a subset
of the cDNA alignments found in the cDNA database (for human and mouse)
or otherfeatures database (all other species).
</li>

</ul>

<h3><a id="cdna" name="cdna">cDNA database</a></h3>

<p>
Human and Mouse have a separate cDNA database, containing alignments of
all species-specific cDNAs to the genome sequence, which serve as source
of biological evidence in the Ensembl annotation strategy. The
alignments are updated every release and should therefore include even
the most recently submitted cDNA sequences.
</p>

<h3><a id="est" name="est">OtherFeatures database</a></h3>

<p>
For human and mouse, the otherfeatures database contains the full set of
species-specific EST alignments to the genome.  For all other species
with enough species-specific data, the otherfeatures database contains
the full set of species-specific cDNA and EST alignments to the genome.

For well-characterised species with a reasonable amount of biological
sequence records as supporting evidence Ensembl provides an independent
EST gene set, which is solely based on EST information.

Please note that Ensembl OtherFeatures databases do not contain genome
sequences. This saves disk space and by connecting to Core and the
OtherFeatures databases simultaneously, it is still possible to retrieve
sequence information.
</p>

<commit_msg>fixed paragraph length<commit_after><html>
<head>
<title>Core databases and API</title>
</head>

<body>

<h1>Ensembl Core and OtherFeatures databases</h1>


<h2>Database Descriptions</h2>


<h3>Core database</h3>

<p>
For each organism supported by Ensembl, a species-specific Ensembl
Core database stores the bulk of annotation information.  Some of the
key features are:
</p>

<ul>
<li>
The unmasked genome sequence is stored on the sequence-level i.e. in
form of BAC clones or whole genome shotgun scaffolds.
</li>

<li>
Assembly information the generate top-level sequences like chromosomes
from sequence-level entities.
</li>

<li>
The non-redundant set of Ensembl gene, transcript and protein models
annotated by the automated genome analysis and
<a href="/info/docs/genebuild/genome_annotation.html">annotation
pipeline</a>.
</li>

<li>
Sequence tagged sites (STS) marker information on physical sequence
and genetic map locations.
</li>

<li>
Cytogenetic banding patterns if a reliable banding pattern has been
established for the organism.
</li>

<li>
Microarray probe set annotation.
</li>

<li>
External references to other databases of biological information.
</li>

<li>
cDNA and protein alignments supporting the transcript models that have
been built. The cDNA alignments found in the core database are a subset
of the cDNA alignments found in the cDNA database (for human and mouse)
or otherfeatures database (all other species).
</li>

</ul>

<h3><a id="cdna" name="cdna">cDNA database</a></h3>

<p>
Human and Mouse have a separate cDNA database, containing alignments of
all species-specific cDNAs to the genome sequence, which serve as source
of biological evidence in the Ensembl annotation strategy. The
alignments are updated every release and should therefore include even
the most recently submitted cDNA sequences.
</p>

<h3><a id="est" name="est">OtherFeatures database</a></h3>

<p>
For human and mouse, the otherfeatures database contains the full set of
species-specific EST alignments to the genome.  For all other species
with enough species-specific data, the otherfeatures database contains
the full set of species-specific cDNA and EST alignments to the genome.
</p>

<p>
For well-characterised species with a reasonable amount of biological
sequence records as supporting evidence Ensembl provides an independent
EST gene set, which is solely based on EST information.
</p>

<p>
Please note that Ensembl OtherFeatures databases do not contain genome
sequences. This saves disk space and by connecting to Core and the
OtherFeatures databases simultaneously, it is still possible to retrieve
sequence information.
</p>


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