very out of date and better described elsewhere

docs/outline.txt

-
-Ensembl
--------
-
-Ensembl is a software system which produces and maintains automatic
-annotation on eukaryotic genomes. The end result is a database of
-genomic sequence with features attached to them: of particular
-importance are gene features which represent protein coding genes in
-the genome. Ensembl copes with rapid updates in data and working draft
-quality genome inherently and provides stable identifiers for genes so
-researches can track the genes of interest across different versions
-of the data.
-
-The Ensembl system is currently being applied to the human genome data
-and is being kept up to date on the current state of the human genome.
-It will in the future be applied to other genomes.
-
-Ensembl provides a number of different data formats so that the
-information contained within it can be easily integrated using
-existing tools. These include EMBL/Genbank formats, GFF and
-GAME-XML. In addition, the entire ensembl database can be mirrored and
-the Ensembl software used to retrieve object-based views of the
-database.
-
-Ensembl analysis is currently based around the following techniques:
-
-	Genscan prediction of proteins
-		BLAST of predicted peptides vs the following databases
-		      protein databases
-		      EST databases
-		      veterbrate cDNA databases
-
-        Assembly of exons which have been confirmed by the BLAST hits
-into gene structures which can span contigs in working draft data.
-
-
-        Repeat Masker repeat prediction
-
-        Pfam analysis of the predicted genes
-
-
-The Ensembl web site is designed to provide an easy to query interface
-into the genome.
-
-
-The following data sources and techniques will be intergrated into Ensembl in
-the future:
-
-         Refined gene prediction using state-of-the art tools.
-
-         Genomic Map data, genetic, radiation hybrid and disease loci
-
-         Bac End data
-
-         Contig Maps.
-
-
-The Ensembl software is designed for a lifetime of around 10 years and
-has been written so that it is portable to other sites and
-maintainable by other people. The Ensembl software is also open
-source, and anyone can use or modify the Ensembl software with almost
-minimal restrictions, both academic and commercial.
-