From dmerrill from ksu.edu Thu Apr 22 10:29:02 2010 From: dmerrill from ksu.edu (Doris Merrill) Date: Thu Apr 22 11:13:33 2010 Subject: [Arthropod] Abstracts Due 5/19 for Arthropod Genomics Symposium Message-ID: ***Print this e-mail from a PDF*** Arthropod Genomics: New Approaches and Outcomes 4th ANNUAL ARTHROPOD GENOMICS SYMPOSIUM June 10 ? 13, 2010, in Kansas City, USA Symposium website: www.k-state.edu/agc/symp2010 We welcome your participation in the 4th Annual Arthropod Genomics Symposium! Two new features have been added to the Symposium website: 1) A list of registered participants, and 2) Roommate matching. You still have time to register and make arrangements to attend!!! Deadlines: Wed., May 19 Poster Abstract Submissions. Six platform presentations will be chosen from submitted poster abstracts. Please follow GUIDELINES posted to symposium website. Wed., May 19 Hotel Reservations at the KC Marriott on the Plaza Wed., May 19 Registration (Registration will continue to be accepted after May 19, if space is available.) REGISTRATION: The registration fee is $395 ($225 for graduate and undergraduate students) on or before Wednesday, May 19, and will include a welcome reception Thursday evening, breakfast and lunch on Friday and Saturday, and breakfast on Sunday. SYMPOSIUM PROGRAM: The symposium sessions will begin Thursday evening, June 10, and continue on Friday and Saturday, with additional events Saturday evening and Sunday morning. Speakers will present new insights from genomic approaches in arthropods and describe the development of tools for genomic analysis. Workshops will be held Thursday prior to the Symposium and Saturday morning. Activities will conclude by noon on Sunday, June 13. ROUNDTABLE DISCUSSION: Sunday morning will highlight a roundtable discussion led by members of the ArthropodBase Consortium regarding the generation of integrated arthropod genome databases and tools for genome projects. Symposium attendees are invited to join the fun as we share our progress by providing feedback on these projects and proposing new possibilities. FUNDING AGENCY PRESENTATIONS: Representatives from national funding agencies will make short presentations about funding philosophies and opportunities within their programs. Following each presentation, the floor will be open for questions and discussion. Speakers include: Alan Christensen, NSF Adriana Costero, NIAID, NIH Mary F. Purcell-Miramontes, USDA, NIFA PRE-SYMPOSIUM WORKSHOP: Thursday afternoon, June 10, 4:00-6:00 pm Navigating NCBI?s resources for insect genomics. Terence Murphy, NCBI/NIH, will provide training on utilizing NCBI?s resources for insect genomics. Topics will include accessing data in the RefSeq and Entrez Gene databases, BLink, BLAST, NCBI?s Map Viewer, and other resources. Issues regarding the submission of data to NCBI and options for linking outside resources to NCBI?s databases will also be discussed. There is no cost to attend this optional workshop, but registration is requested. WORKSHOP/SEMINAR: Saturday morning, June 12, 10:00-11:30 am MAKER: Genome annotation made easy. Carson Holt, University of Utah, will provide a basic overview of MAKER and demonstrate both the command line version and the new online MAKER Web Annotation Service (MWAS). MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. Several use-case scenarios with example data and results will also be presented. ORGANISM MEETINGS: Friday afternoon/evening, June 11, 5:15-? p.m. Meet with scientists who are also working with your organism of interest during small group gatherings. Group leaders will be identified to coordinate topics and lead discussions. Additional information will be posted to the conference website as details are finalized. Keynote Speaker: *Nora J. Besansky, University of Notre Dame Population genomics of adaptation and speciation in malaria?s vector Featured Speakers: *Michael Akam, University of Cambridge, United Kingdom The genome of the Geophilomorph centipede, Strigamia maritima *Scott J. Emrich, University of Notre Dame Opportunities and challenges of non-model transcriptome sequencing: From corn to wild butterflies and moths *Matthew Hudson, University of Illinois at Urbana-Champaign Exploring the evolution of social behavior using genome sequencing and analysis *Anthony A. James, University of California Message in a battle, using whole genome expression analyses to fight vector-borne diseases *Michael R. Kanost, Kansas State University Functional genomics of cuticle sclerotization in Tribolium castaneum *Fabrice Legeai, INRA, Rennes, France Prediction and analyses of non coding RNA sequences in the pea aphid genome *Barry R. Pittendrigh, University of Illinois at Urbana-Champaign The Body Louse genome project *Patrick D. Schloss, University of Michigan Bugs within bugs: Understanding the influence of the microbiome on arthropod health *Christian Schl?tterer, Vetmeduni Vienna, Austria Next generation sequencing in population genetics: From experimental evolution to gene expression *Zhijian Jake Tu, Virginia Tech Anopheles stephensi genome assembly and transcriptome analysis *John (Jack) H. Werren, University of Rochester Functional and evolutionary insights from the genomes of three parasitoid Nasonia species *Evgeny M. Zdobnov, University of Geneva, Switzerland Genomics in the light of evolution VENUE: The symposium will take place at the Kansas City Marriott on the beautiful Country Club Plaza. Participants are invited to dine Saturday night at an optional banquet at the BRIO Tuscan Grille. INFORMATION: Visit our website, www.k-state.edu/agc/symp2010, for complete details and brochure. Add your name to the Symposium mailing list, by sending your contact information to dmerrill@k-state.edu. QUESTIONS: Contact us at (785) 532-3482 or dmerrill@ksu.edu. Please share this announcement with colleagues and students! SPONSOR: Center for Genomic Studies on Arthropods Affecting Human, Animal and Plant Health, Kansas State University Susan J. Brown, Professor Director, Center for Genomic Studies on Arthropods Affecting Human, Animal and Plant Health and Robin E. Denell, Distinguished Professor Chair, AGC Symposium Organizing Committee by Doris Merrill, Program Coordinator K-State Arthropod Genomics Center Division of Biology, Kansas State University 116 Ackert Hall, Manhattan, KS 66506-4901 (785) 532-3482, dmerrill@k-state.edu www.k-state.edu/agc From gilbertd from net.bio.net Sat Apr 24 14:55:39 2010 From: gilbertd from net.bio.net (Don Gilbert) Date: Sat Apr 24 14:56:46 2010 Subject: [Arthropod] Daphnia pulex Genes 2010 (beta3) Message-ID: <201004241955.o3OJtdi07222@net.bio.net> Dear arthropod enthusiasts, There is a new, improved gene prediction/evidence set for Daphnia pulex, in a beta release, for those interested. Your comments to improve these are desired. This is a much improved gene set. While there are many more genes, most are supported by evidence. Protein homology evidence is extensive now, and suggests that Daphnia's gene set is one of the most complete among arthropods, with more Human orthologs than any other available arthropod genome. Notable stats for this Daphnia Genes2 set vs the 2007 official gene set 1: * Daphnia2 recovers 82% of protein homology, versus 42% for Daphnia1 * Daphnia2 recovers 90% of ESTs, versus 75% for Daphnia1 * Daphnia2 recovers 66% (5Mb) of genome tile expression not in Daphnia1 Daphnia has best matches and longest alignments to human and other model eukaryote gene sets (Tribolium has the best of the insects). This update improves on this. Best matches to Human genes among 14 arthropod genomes: Daphnia2 has 44% of these, vs 21% for Daphnia1. Ixodes has 15%, Tribolium has 10%, and a slim 2% for Drosophila mel. Alignment to Human genes: Daphnia2 averages 191 aminos, 188 aa for Daphnia1 187 aa for Tribolium, and 175 aa for Drosophila. Percent of 20,000 Human genes found: 71% for Daphnia2, 69% for Daphnia1, 68% for Tribolium, 66% for DrosMel There are problems yet in this gene set that I will fix; a final version may be out in a few months. Find these annotated genes in GFF and protein fasta formats here http://server7.wfleabase.org/prerelease4/gene-predictions/ Also see this poster from the recent Daphnia Genomics meeting with comments on these new gene predictions. http://wfleabase.org/docs/all-docs/daphnia-genomes-crossroads10.pdf - Don Gilbert -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd@indiana.edu--http://marmot.bio.indiana.edu/