Annotation of DMA sequences is an essential prerequisite for understanding the biology of genes and gene products in any organism. An annotation is any feature that can be tied to genomic sequence, such as an exon, transcript, promoter, or transposable element. The highest-quality annotation is obtained by combining automated sequence analysis results with the expert knowledge of biologists. Apollo is a cross-platform annotation editing tool that streamlines this process by providing an interactive graphical display that allows biologists to view many different computational analyses of a genomic region and use them, together with their knowledge of direct experimental results, to create and refine detailed annotations. Apollo is an Open Source Java application that is easy to install and run on any platform. Since its initial release in 2002, Apollo has become one of the most widely used annotation editors. Factors contributing to its success include its intuitive, interactive user interface; configurability; simple installation process; extensive documentation; highly responsive mailing list; extensibility; and an Open Source code-base. It has been downloaded thousands of times, and a wide variety of both academic and commercial research groups have modified or extended it to suit their individual needs (see Appendix 1), thereby saving countless hours of development time We are requesting funding for continued support and improvement of this valuable software resource Our goals include making Apollo fully aware of the Sequence Ontology, to better support community-wide annotation of diverse organisms; designing new configuration interfaces to simplify the process of loading data from different sources and setting display preferences; and adding two new specialized editors: a multiple alignment transcript viewer and editor, to allow gene models to be modified in direct reference to alignment data; and a repetitive element editor. We also plan to offer more support and outreach, including workshops and on-site visits to train biologists to use Apollo and show software developers how to integrate their existing tools into Apollo's extensible framework. The work in this proposal will be performed as a collaboration between Lawrence Berkeley National Laboratory (LBNL) and The Arabidopsis Information Resource (TAIR) at the Carnegie Institution, with LBNL supplying the bulk of the software development and Carnegie providing targeted software development resources and annotation expertise. ? ? ?
