unison-tutorial

Unison TutorialReece Hart2006-05-12 Tutorial Outline● Introduction– data sources, algorithms, update scheme● Schema– overview, design themes, critical tables● Access– web pages, command line tools, perl API, psql● Example Queries– Finding sequences– Finding parameters– Getting predictions for a sequence– Mining for sequence based on predictions– Tips● Future Plans What Can I Do With Unison?● Retrieve sequence analysis for a single sequence.● Mine for sequences based on predicted features, sequence origins, taxonomy, patents, orthology, and structure.● Find all sources of a single sequence.● Find patents for a sequence.● Locate sequence variations relative to domains and in structure.● Build new tools. Design Goals● Sequences are stored non-redundantly.– eliminates redundant computation and analysis– Results are keyed to sequences, parameters, and optionally a model.– Sequences are immutable and therefore results are never stale.– Sequences are linked to their origins and aliases.● Fast, reliable, differential updates.● Multiple result sets for different invocations● Make no assumptions and provide no interpretations.● Synopses of prediction results only, but and enable regeneration of results. Unison Contents● Non-redundant Sequences– UniProtKB/Swiss-Prot, IPI, Genengenes, Genehub representative sequences, RefSeq, Curagen, Incyte, ..., Ensembl ab initio, miscellaneous fragments● Non-redundant Results– Pfam, TMHMM, ...