<commit_before><html>
<head>
<meta name="author" content="helpdesk" />
<meta name="navigation" content="Data" />
<meta name="update-period" content="2005-05-27" />
<title>FTP Directory Structure</title>
</head>

<body>

<h2>FTP Directory Structure</h2>


<h3 class="boxed">Introduction</h3>

<p>
The Ensembl FTP site provides biological sequence databases suitable for
large-scale local sequence similarity search approaches, as well as MySQL table
dumps of all underlying Ensembl databases.
These table dumps are suitable for import into relational database management
systems and allow
<a href="../software/website/installation/index.html">installation</a>
of complete Ensembl mirror sites.
</p>

<p>
<strong>Please note:</strong>
Ensembl supports downloading of many correlation tables via the highly
customisable
<a href="http://www.ebi.ac.uk/biomart/">BioMart</a> data mining tool.
You may find exploring this web-based data mining tool easier than extracting
information from our normalised database dumps.
</p>

<p>
The URL
<a href="ftp://ftp.ensembl.org/pub/" target="external">ftp://ftp.ensembl.org/pub/</a> is the basis of the directory structure outlined below.
The structure is also described in the FTP site
<a href="ftp://ftp.ensembl.org/pub/README">README</a>.
The latest data sets for each species are available via directories prefixed
'<strong>current_</strong>'.
For example 'current_mouse' will always point to the latest data release for
the mouse.
</p>


<h3 class="boxed">Species Directories</h3>

<p>
All species directories have the following basic structure, although not all
information is neccessarily available for each species.
</p>

<pre>

-- species
   |
   |-- data
       |
       |-- emf            Alignment dumps in EMF format
       |   |
       |   |-- variation    * resequencing data
       |
       |-- fasta          Gene predictions in FASTA database format
       |   |
       |   |-- cdna         * Transcript (cDNA) predictions
       |   |-- dna          * Genomic DNA in assembled entities
       |   |-- pep          * Translation (peptide) predictions
       |   |-- rna          * Non-coding RNA predictions
       |
       |-- flat files     Gene predictions annotated on genomic DNA slices of 1 Mb.
       |   |
       |   |-- embl         * EMBL format
       |   |-- genbank      * GenBank format
       |
       |-- gtf            Gene annotation in GTF format
       |
       |-- mysql          MySQL database table text dumps
           |
           |-- core       General genome annotation information
           |
           |                * Genome sequence assembly
           |                * Ensembl gene predictions
           |                * Ab initio gene predictions
           |                * Marker information
           |                * ...
           |
           |-- otherfeatures  Additional genome annotation
           |
           |                * Gene predictions based on EST information
           |                * ...
           |
           |-- variation  Genetic variation information
           |-- vega       Manually curated gene sets
           |-- cdna       cDNA to genome alignments based on the latest EMBL database

</pre>


<h3 class="boxed">Multi-species Directories</h3>

<p>
The 'multi-species' directories contain databases not directly linked to single
species data or which contain link data between species.
</p>

<pre>

-- multi-species
   |
   |-- data
       |
       |-- emf                      Alignment dumps in EMF format
       |   |
       |   |-- pecan                  * Pecan whole genome multiple alignments
       |   |                            with conservation scores for selected sets
       |   |
       |   |-- protein_trees          * protein trees and protein multiple alignments
       |   |                            underlying orthologue/paralogue predictions
       |
       |
       |-- mysql                    MySQL database table text dumps
           |
           |-- ensembl_compara      Cross-species comparative genomics data:
           |
           |                          * Orthologue/paralogue predictions
           |                          * Protein families
           |                          * Whole genome alignments
           |                          * Synteny information
           |
           |-- ensembl_go           Gene Ontology database
           |
           |-- ensembl_web_user_db  SQL table defintion for server-side user config database
           |
           |-- ensembl_website      Ensembl web site database:
           |                          * Context-sensitive help articles
           |                          * News articles
           |                          * Mini-ads
</pre>


<h3 class="boxed">Mart Directory</h3>

<p>
The 'mart' directory contains table dumps of the databases underlying the
<a href="http://www.ebi.ac.uk/biomart/">BioMart</a> data mining tool.
</p>

<pre>

-- mart
   |
   |-- data
       |
       |-- mysql              MySQL database table text dumps
           |
           |-- compara_mart_homology     Orthologue/paralogue predictions
           |-- compara_mart_multiple_ga  Constrained elements predictions
           |-- compara_mart_pairwise_ga  Whole genome pairwise alignments
           |-- ensembl_mart              Cross-species data mining tables
           |-- genomic_features_mart     Clone data sets
           |-- sequence_mart             Genome sequences
           |-- snp_mart                  Genetic variation information
           |-- vega_mart                 Manually curated gene sets

</pre>


<!--
<p>
Please note that file name substitution or globbing has been turned off in the
FTP server so that you cannot use meta characters or wildcards for pattern
matching in your FTP requests.
Smart clients like
<a href="http://directory.fsf.org/wget.html" target="external">GNU wget</a>
or mirroring software should be able to work around this.
</p>
-->

<!--<commit_msg>updated due to changes for release 47<commit_after><html>
<head>
<meta name="author" content="helpdesk" />
<meta name="navigation" content="Data" />
<meta name="update-period" content="2005-05-27" />
<title>FTP Directory Structure</title>
</head>

<body>

<h2>FTP Directory Structure</h2>


<h3 class="boxed">Introduction</h3>

<p>
The Ensembl FTP site provides biological sequence databases suitable for
large-scale local sequence similarity search approaches, as well as MySQL table
dumps of all underlying Ensembl databases.
These table dumps are suitable for import into relational database management
systems and allow
<a href="../software/website/installation/index.html">installation</a>
of complete Ensembl mirror sites.
</p>

<p>
<strong>Please note:</strong>
Ensembl supports downloading of many correlation tables via the highly
customisable
<a href="http://www.ebi.ac.uk/biomart/">BioMart</a> data mining tool.
You may find exploring this web-based data mining tool easier than extracting
information from our normalised database dumps.
</p>

<p>
The URL
<a href="ftp://ftp.ensembl.org/pub/" target="external">ftp://ftp.ensembl.org/pub/</a> is the basis of the directory structure outlined below.
The structure is also described in the FTP site
<a href="ftp://ftp.ensembl.org/pub/README">README</a>.
The latest data sets are available via directories prefixed
'<strong>current_</strong>'.
For example 'current_embl' will always point to the latest data release files in EMBL format.
</p>


<h3 class="boxed">FTP Site Directories</h3>

<p>
The FTP directory has the following basic structure, although not all
information is neccessarily available for each species.
</p>

<pre>

   |-- embl	      Gene predictions annotated on genomic DNA slices of 1 Mb in EMBL format.
   |   | 
   |   |-- species
   |
   |
   |-- emf     	      Alignment dumps in EMF format
   |   | 
   |   |-- pecan                  * Pecan whole genome multiple alignments
   |   |                            with conservation scores for selected sets
   |   |-- ensembl_compara        * protein trees and protein multiple alignments
   |   |                            underlying orthologue/paralogue predictions
   |   |--species_variation       * resequencing data
   |
   | 
   |-- fasta	      Gene predictions in FASTA datatabase format
   |   |
   |   |--species
   |      |
   |      |-- cdna         * Transcript (cDNA) predictions
   |      |-- dna          * Genomic DNA in assembled entities
   |      |-- pep          * Translation (peptide) predictions
   |      |-- rna          * Non-coding RNA predictions
   |
   |            
   |-- genbank	      Gene predictions annotated on genomic DNA slices of 1 Mb in GenBank format.
   |   | 
   |   |-- species
   |
   |
   |-- gtf	      Gene annotation in GTF format
   |
   |-- mysql          MySQL database table text dumps
       |
       |-- core       General genome annotation information
       |
       |                * Genome sequence assembly
       |                * Ensembl gene predictions
       |                * Ab initio gene predictions
       |                * Marker information
       |                * ...
       |
       |-- otherfeatures  Additional genome annotation
       |
       |                * Gene predictions based on EST information
       |                * ...
       |
       |-- variation  Genetic variation information
       |-- vega       Manually curated gene sets
       |-- cdna       cDNA to genome alignments based on the latest EMBL database
       |
       |-- ensembl_compara      Cross-species comparative genomics data:
       |
       |                          * Orthologue/paralogue predictions
       |                          * Protein families
       |                          * Whole genome alignments
       |                          * Synteny information
       |
       |-- ensembl_go           Gene Ontology database
       |
       |-- ensembl_web_user_db  SQL table defintion for server-side user config database
       |
       |-- ensembl_website        Ensembl web site database:
       |                            * Context-sensitive help articles
       |                            * News articles
       |                            * Mini-ads
       |-- compara_mart_homology     Orthologue/paralogue predictions
       |
       |-- compara_mart_multiple_ga  Constrained elements predictions
       |
       |-- compara_mart_pairwise_ga  Whole genome pairwise alignments
       | 
       |-- ensembl_mart              Cross-species data mining tables
       |
       |-- genomic_features_mart     Clone data sets
       |
       |-- sequence_mart             Genome sequences
       |
       |-- snp_mart                  Genetic variation information
       |
       |-- vega_mart                 Manually curated gene sets

</pre>

<!--
<p>
Please note that file name substitution or globbing has been turned off in the
FTP server so that you cannot use meta characters or wildcards for pattern
matching in your FTP requests.
Smart clients like
<a href="http://directory.fsf.org/wget.html" target="external">GNU wget</a>
or mirroring software should be able to work around this.
</p>
-->

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