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Trypasosoma brucei README 


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Table of Contents
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1. Trypanosoma brucei genome sequencing project

2. File format

3. Data Access

4. Contacts
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1. Trypanosoma brucei genome sequencing project
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T. brucei, the protozoan responsible for African Sleeping Sickness, possesses a 
two-unit genome, a nuclear genome and a mitochondrial (kinetoplast) 
genome with a total estimated size of 35Mb/haploid genome. The nuclear genome is split 
into three classes of chromosomes according to their size on pulse filed gel 
electrophoresis, 11 megabase chromosomes (0.9-5.7 Mb), intermediate (300-900 kb) and 
minichromosomes (50-100 kb).  

The 11 chromsomes are being sequenced by The Wellcome Trust Sanger Institute and TIGR 
as follows

   1     Sanger
   2-8   TIGR
   9-11  Sanger

IMPORTANT NOTE: The file gene_association.GeneDB_Tbrucei only contains gene associations 
for the chromsomes sequenced at the Wellcome Trust Sanger Institute.

2. File format
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The file format is based on the the guidelines provided by the Gene Ontology
Consortium (www.geneontology.org) with several   

1.  DB 
    Database from which annotated entry has been taken.
    Here: GeneDB_Tbrucei is used to signify that the data will eventually be is housed 
    in the T. brucei at
    GeneDB (http://www.genedb.org/genedb/tryp/)
    
2.  DB_Object_ID
    A systematic gene name is used as a unique identifier to access gene pages
    in the DB is normally used for the item being annotated. To access each gene page,
    append the Systematic id to the following URL:
    http://www.genedb.org/genedb/Search?organism=tryp&name=
   
    
3.  DB_Object_Symbol
    The systematic gene name is currently used to identify gene pages thus, 
    DB_Object_Symbol and DB_Object_ID are equivalent.
    
4.  NOT
    Rarely used; indicates that a GO assignment is not appropriate despite some evidence 
    to the contrary,  see main GO documentation.
    
5.  GOid
    The GO identifier for the term attributed to the DB_Object_ID.
    Example: GO:0005625
    
6.  DB:Reference
    Reference cited to support the attribution. This is pre-publication data, 
    after publication this column will contain a PubMed id for a supporting 
    reference for the attributions
    
7.  Evidence
    See main documentation
    
8.  With
    Here: Currently not applicable, always empty.
    
9.  Aspect
    One of the three ontologies: P (biological process), F (molecular function) 
    or C (cellular component).
    Example: P
    
10. DB_Object_Name
    Here: Currently not applicable.  Contains the same information as column 2.  
    Will soon contain details of the closest Drosophila homologue for reference 
    purposes

11. Synonym
    Here: Currently not applicable, always empty.
    
12. DB_Object_Type
    What kind of entity is being annotated.
    Here: always 'gene'   
    
13. Taxon_ID
    Identifier for the species being annotated.
    Here:
    taxon:5833

14. Date
    Date that the analysis was performed


3. Data Access
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All sequences analysed are available from 

   http://www.sanger.ac.uk

4. Contacts
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   Matt Berriman, mb4@sanger.ac.uk
   Christiane Hertz-Fowler, chf@sanger.ac.uk