Data types available for searching

• Sequence reads
  These are the individual sequence reads, generally 500-600 bp in length. The sequence read has the shotgun clone id and either "q1c" or "p1c" (for either forward or reverse primer) in its name.
• Contig sequences
  Assembled contigs taken at 3x coverage and their automated annotation are now available via GeneDB. In addition to this, all available contig sequence > 2kb are regularly posted on the ftp site.
  • Contig sequences represent secondary sequence data, in that they are the condensation of a number of shotgun reads. Contig reflect more reliably the finished sequence data because the depth of coverage of assembled shotgun reads ensures that the majority of ambiquities are identified and at least partially resolved. This is not to say that contigs do not contain insertion and/or deletion events, usually as a conseqeunce of the algorithim used to create a consensus. Please not, that currently the Sanger Institute is unable to track contigs through assembly and therefore, contig id's will change.
  • Individual contig sequences which are highlighted by Blast analysis can be retrieved by following the 'Sequence' link in the returned HTML page.
  • Only contigs greater than 2 kb are present in the Blast searchable dataset.