We have recently developed a hight throughput windows based toolkit that utilizes sequence similarity to define functional annotations. This software assigns Gene Ontology, Enzyme Commission and KEGG pathways to sequence data utilizing a custom curated database based upon GOA. It can be downloaded for free at our website along with the formatted database. We also have a user freindly distributed BLAST application known as W.ND BLAST (windy BLAST) also available free. It has complete gui's for database engineering, blast engines, as well as a very nice output viewer, curator, annotation engine.

Hi, How does your tool perform compared with other academia-open source tools for GO annotation? Have you considered integrating also literature serarch in your software?
Adolfo

Hi for unknown sequences in high throughput situations it performs very well. WIth an integrated distributed BLAST algorithm performance is unparalleled for a locally installable free solution.

We have utilized text mining but this does not enhance or improve the results just adds to them.

Currently, we do not support an append reference feature within HT-GO-FAT though utilizing a xref such as pubmed2go or a integrated web call to pubmed would be easy enough.

We just released a new version that is freely downloadable. A new curated database will be release next week as well with over 1.5 million sequences.