1. BAC Sequencing and Annotation: Procedure Updates and New Tools Robert Buels

2. Talk Sections  New BAC sequence submission guidelines  Distributed annotation project  Tool on SGN for reserving BACs for mapping to IL lines

3. BAC Submissions  Now: must submit to GenBank BEFORE submitting to SGN  Include BAC name and TOMGEN keyword  updated guidelines at  Need GenBank accessions for the ITAG pipeline http://docs.google.com/View.aspx?docid=dggs4r6k_1dd5p556

4. BAC Submissions  GenBank entry must contain:  BAC name in DEFINITION field, adhering to SOL Bioinformatics Guidelines  TOMGEN keyword somewhere in COMMENT field (this makes searches for all of our sequences easy!)  Hurray, many have already done it!  Also notify SGN (email accessions, or resubmit BAC tarfiles)

5. BAC Distributed Annot. ITAG International Tomato Annotation Group alignments de novo gene pred. seqs (GB/EMBL/DDBJ) rpsblas t RELEASE gbrowse, datasets (CDS, pep, nr), etc. etc... blastp signal p interpro

6. BAC Annotation ITAG Distributed Pipeline

7. BAC Distributed Annot. ITAG Distributed Pipeline 1. CAB dl seqs 2. CAB ul EST alignments 3. Ghent dl alignments, etc. 4. Ghent ul Eugene results 5. MIPS dl Eugene results 6. MIPS ul GO assignments

8. Assign IL Mapping  Log in to SGN (must be sequencer)  Go to your BAC's detail page  Use select box to assign BAC for IL

9. End end of main presentation

10. ITAG Pipeline Resources  The Wiki  The Status Page  The Status Service

11. The Wiki  List of ITAG members (add yourself!)  Full documentation of everything  Document your analysis http://www.ab.wur.nl/TomatoWiki

12. The Status Page http://www.sgn.cornell.edu/sequencing/itag/status_html.pl

13. The Status Web Service  List pipelines ( lp )  List batches ( lb )  List analyses ( la )  List sequences ( lbs )  Check status of analysis ( astat ) http://www.sgn.cornell.edu/sequencing/itag/status.pl http://www.ab.wur.nl/TomatoWiki/PipelineStatusWebService