ISMB 2008

Short Abstract: We have developed a new algorithm, called TTell, to reliably predict positions of transcription start sites. Our method is based on availability of complete genome sequences, large numbers of 5’ expressed sequence tags, tiling arrays and growing collections of transcription factors. Our method allows for more accurate identification of TSS.

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Poster I04

An Expanding Asset for Pathogen Informatics - The Enteropathogen Resource Integration Center (ERIC), A NIAID Bioinformatics Resource Center for Biodefense and Emerging/Re-Emerging Infectious Disease

John Greene- SRA International, Inc.

David Pot (SRA International, Health Research Informatics); Jon Whitmore (SRA International, Health Research Informatics); Matthew Shaker (SRA International, Health Research Informatics); Joel Fedorko (SRA International, Health Research Informatics); Kamini Joshi (SRA International, Health Research Informatics); Panna Shetty (SRA International, Health Research Informatics); Silpa Nanan (SRA International, Health Research Informatics); Jeyanthi Thangiah (SRA International, Health Research Informatics); Sam Zaremba (SRA International, Health Research Informatics); Guy Plunkett III (University of Wisconsin, Madison, Genetics); Jeremy Glasner (University of Wisconsin, Madison, Genetics); Bradley Anderson (University of Wisconsin, Madison, Genetics); David Baumler (University of Wisconsin, Madison, Genetics); Bryan Biehl (University of Wisconsin, Madison, Genetics); Valerie Burland (University of Wisconsin, Madison, Genetics); Eric Cabot (University of Wisconsin, Madison, Genetics); Eric Neeno-Eckwall (University of Wisconsin, Madison, Genetics); Bob Mau (University of Wisconsin, Madison, Genetics); Paul Liss (University of Wisconsin, Madison, Genetics); Michael Rusch (University of Wisconsin, Madison, Genetics); Frederick Blattner (University of Wisconsin, Madison, Genetics); Nicole Perna (University of Wisconsin, Madison, Genetics);

Short Abstract: ERIC (www.ericbrc.org) is an NIAID Bioinformatics Resource Centers focused on enteropathogens, and continues to evolve to provide analysis tools for integrated access to data on 78 genomes to date. We provide curated genome annotation of these organisms with evidence codes, and tools for comparative genomics, microarray analysis, and text mining.

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Poster I05

Reference Genomes and the GO

Judith Blake- The Jackson Laboratory

Pascale Gaudet (Northwestern University, Center for Genetic Medicine); Rex Chilsolm (Northwestern University, Center for Genetic Medicine); GO Reference Genome Annotation Participants (Gene Ontology, Consortium);

Short Abstract: The GO Reference Genome Project is a shared annotation effort among the GO Consortium members who provide annotations for nine model organisms such as mouse, fly and yeas. The GO curators of the Model Organism Databases are coordinating their efforts in providing comprehensive annotations for the set of target genes.

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Poster I06

ProSOM: Core promoter prediction based on unsupervised clustering of DNA physical profiles

Thomas Abeel- VIB - Ghent University

Yvan Saeys (VIB - Ghent University, Department Of Plant Systems Biology); Pierre Rouzé (Department Of Plant Systems Biology, Department Of Plant Systems Biology); Yves Van de Peer (Department Of Plant Systems Biology, Department Of Plant Systems Biology);

Short Abstract: We present ProSOM, a novel core promoter prediction program. We used self organizing maps to distinguish promoter sequences from other sequences in the genome and obtain state-of-the-art performance using a biologically sound validation. Core promoter prediction can provide guidance for experimental work or provide additional information for genome annotation projects.

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Poster I07

Analysis of the annotation of draft whole genome assemblies

Alexandre Souvorov- National Center for Biotechnology Information

Yuri Kapustin (National Center for Biotechnology Information, IEB); Boris Kiryutin (National Center for Biotechnology Information, IEB); Vyacheslav Chetvernin (National Center for Biotechnology Information, IEB); Tatiana Tatusova (National Center for Biotechnology Information, IEB); David Lipman (National Center for Biotechnology Information, IEB);

Short Abstract: Draft whole genomes pose special problems for the annotation processes. To assess the quality of genome annotation we analyzed several vertebrate genomes.
We have performed the analysis of the frame shifted genes in the context of genome assembly and have shown a correlation between frameshift locations and gaps of coverage.

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Poster I08

KinomeBrowser: a graphical tool to explore kinomes

Neil Saunders- University of Queensland

Bostjan Kobe (University of Queensland, School of Molecular and Microbial Sciences);

Short Abstract: KinomeBrowser is a tool for exploration of the kinome: the protein kinases encoded in a genome and their putative substrates. It provides annotation of a genome with kinome-specific features and a user-friendly graphical interface to these data built using the Generic Genome Browser.

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Poster I09

Recent developments in high-throughput transcriptomics with X:MAP and exonmap

Michal Okoniewski- Functional Genomics Center Zurich

Tim Yates (Paterson Institute, Bioinformatics); Danny A Bitton (Paterson Institute, Bioinformatics); Crispin J Miller (Paterson Institute, Bioinformatics);

Short Abstract: Recent developments in the X:MAP/exonmap system for Affymetrix exon arrays made it even more useful for various transcriptomics tasks. The phenomena that may be studied include new isoforms, alternative splicing, validation of legacy expression data. The approach was also successfully used in the data integration between transcriptomics and proteomics.

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Poster I10

The correlation of domain loss and nonsense-mediated decay due to alternative splicing

Younghee Lee- University of Chicago

No additional authors

Short Abstract: Alternative splicing yields diverse mRNA structures from a single primary transcript. During this process, a functional domain can be deleted. Alternative splicing is likely to introduce PTC into domain-loss transcripts in order to remove them, as transcripts which lost their domains completely are undesirable products due to abnormal splicing.

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Poster I11

Discovering Relationships among Dispersed Repeats using Spatial Association Rule Mining

Surya Saha- Mississippi State University

Susan Bridges (Mississippi State University, Department of Computer Science and Engineering); Zenaida Magbanua (Mississippi State University, Department of Plant & Soil Sciences); Dan Peterson (Mississippi State University, Department of Plant & Soil Sciences);

Short Abstract: While a number of algorithms are available for discovering novel dispersed repeats, a significant amount of analysis is required to characterize the new elements. We present an algorithm for mining spatial relationships among ab initio identified repeat families to yield clusters of repeat regions on the genome.

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Poster I12

The Ensembl Gene Annotation Pipeline

Laura Clarke- The Welcome Trust Sanger Insitute

Browen Aken (The Welcome Trust Sanger Insitute, Informatics); Susan Fairley (The Welcome Trust Sanger Insitute, Informatics); Julio Banet (The Welcome Trust Sanger Insitute, Informatics); Felix Kokochiski (The Welcome Trust Sanger Insitute, Informatics); Amonida Zadissa (The Welcome Trust Sanger Insitute, Informatics); Sarah Dyer (The Welcome Trust Sanger Insitute, Informatics); Kevin Howe (The Welcome Trust Sanger Insitute, Informatics); Simon White (The Welcome Trust Sanger Insitute, Informatics); Jan Vogel (The Welcome Trust Sanger Insitute, Informatics); Valerie Curwen (The Welcome Trust Sanger Insitute, Informatics); Stephen Searle (The Welcome Trust Sanger Insitute, Informatics); Tim Hubbard (The Welcome Trust Sanger Insitute, Informatics); Michael Schulster (The European Bioinformatics Institute, Ensembl);

Short Abstract: The Ensembl Gene annotation pipeline is used to annotate over 30 species from over a wide evolutionary spectrum. In the last year both new code developments and access to new evidence types have allowed us to improve the quality of our annotation, particularly for the Human and Mouse gene sets

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Poster I13

A Genome Grid for Finding new Bug Genes

Donald Gilbert- Indiana University

No additional authors

Short Abstract: Genome annotation and finding novel genes is lagging the needs of many new genomes. Gene duplication and genome tile expression help address this in Arthropod genomes. Rapid genome analysis pipelines for NSF TeraGrid are developed, as part of GMOD (www.gmod.org/Genome_grid).

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Poster I14

Tissue specific transcriptome landscape analysis of the early mouse embryo

Martin Werber- Max Planck Institute For Molecular Genetics

Phillip Grote (Max Planck Institute For Molecular Genetics, Max Planck Institute For Molecular Genetics); Lars Wittler (Max Planck Institute For Molecular Genetics, Max Planck Institute For Molecular Genetics); Bernhard Herrmann (Max Planck Institute For Molecular Genetics, Max Planck Institute For Molecular Genetics);

Short Abstract: We dissected tissues out of mouse embryos. For each we generated dsDNA from totalRNA and subjected the resulting tissue-specific libraries to sequencing using Illumina/Solexa® platform. Our analysis of digital expression profiles creates an unbiased catalog of tissue specific coding transcripts, including splice variants, and potential ncRNA, including miRNA precursors.

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Poster I15

Bioinformatics to support the sequencing of Brassica rapa chromosomes A2 and A10.

Matthew Links- Agriculture and Agri-food Canada

Steve Karcz (Agriculture and Agri-food Canada, BioProducts and Bioprocessing); Jacek Nowak (National Research Council of Canada, Plant Biotechnology Institute); Andrew Sharpe (National Research Council of Canada, Plant Biotechnology Institute); Isobel Parkin (Agriculture and Agrifood Canada, BioProducts and Bioprocessing);

Short Abstract: Using the software packages APED and Gbrowse we demonstrate an automated system to warehouse, assemble and display DNA sequence for BAC sequencing. We demonstrate the use of the system to support Canadian efforts to sequence chromosomes A2 and A10 from Brassica rapa utilizing both Sanger and Next-Generation (GS-FLX) sequence data.

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Poster I16

Using Subsystems to Predict Contig-spanning Genes in Bacterial Genomes

Jie Zhou- Northern Illinois University

Minmei Hou (Northern Illinois University, Computer Science); Gordon Pusch (Fellowship for Interpretation of Genomes, University of Chicago, Computation Institute); Folker Meyer (Argonne National Lab, University of Chicago, Computation Institute);

Short Abstract: Recent sequencing technologies provide efficient sequencing yet produce short sequence fragments. We propose an algorithm that identifies contig-spanning genes for prokaryotic genomes and uses the subsystem framework to support and validate the predictions. Experiments were done on eight strains of Listeria with promising results.

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Poster I17

Novel algorithms for structural annotation of prokaryote genomes

Nan Wang- Mississippi State University

Shane Burgess (Mississippi State University, College of Veterinary Medicine); Mark Lawrence (Mississippi State University, College of Veterinary Medicine); Bindu Nanduri (Mississippi State University, College of Veterinary Medicine); Fiona McCarthy (Mississippi State University, College of Veterinary Medicine); Changhe Yuan (Mississippi State University, Department of Computer Science and Engineering); Susan Bridges (Mississippi State University, Department of Computer Science and Engineering);

Short Abstract: Genome structural annotation is the major goals of genomics research and is accomplished by computational pipelines, which have many shortcomings. Proteomic data can be used to confirm gene identifications from computational methods and to correct mistakes. We have developed a novel algorithm using MS/MS peptides for structural annotation of genomes.

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Poster I18

Bioinformatics analysis of Xanthomonas vasicola pathovar musacearum draft genome

Mtakai Ngara- International Institute of Tropical Agriculture(IITA)

Dong-Jin Kim (International Institute of Tropical Agriculture(IITA), Biotechnology); Etienne de Villiers (International Institute of Livestock Research(ILRI), Bioinformatics);

Short Abstract: The draft genome of Xanthomonas Vasicatoria pathovar musecearum(Xvm) was annotated using TIGR annotation engine and is currently undergoing manual annotation.Through the analysis, genes encoding virulence factors have been characterized and comparative genome analysis will unravel the genetic factors for host specificity and Xvm genome dynamics.

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Poster I19

Validation and Addition of Functional Information to Manually Annotated Splice Variants of Coding Genes

Adam Frankish- Wellcome Trust Sanger Institute

Jonathan Mudge (Wellcome Trust Sanger Institute, Human and Vertebrate Analysis and Annotation Group); Michael Tress (Spanish National Cancer Research Centre (CNIO), Structural Computational Biology Group); Robert Finn (Wellcome Trust Sanger Institute, Pfam Group); James Gilbert (Wellcome Trust Sanger Institute, Informatics); Roy Storey (Wellcome Trust Sanger Institute, Informatics); Laurens Wilming (Wellcome Trust Sanger Institute, Human and Vertebrate Analysis and Annotation Group); Alexandre Reymond (University of Lausanne, Center for Integrative Genomics); Alfonso Valencia (Spanish National Cancer Research Centre (CNIO), Structural Computational Biology Group); Stylianos Antonarakis (University of Geneva Medical School and University Hospitals of Geneva, Department of Genetic Medicine and Development); Roderic Guigó (Centre for Genomic Regulation, Bioinformatics and Genomics); Alex Bateman (Wellcome Trust Sanger Institute, Pfam Group); Jennifer Harrow (Wellcome Trust Sanger Institute, Human and Vertebrate Analysis and Annotation Group); Tim Hubbard (Wellcome Trust Sanger Institute, Informatics);

Short Abstract: The HAVANA group produce high quality, manual annotation of protein-coding genes, identifying large numbers of splice variants, many of which contain apparently valid CDSs. We are collaborating with the Biosapiens consortium and Pfam group to investigate the structural and functional implications of alternative splicing.

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Poster I20

DETERMINING PRINCIPAL GENE PRODUCTS

Michael Tress- CNIO

Jan-Jaap Wesselink (CNIO, Structural Biology and Biocomputation); Alfonso Valencia (CNIO, Structural Biology and Biocomputation); Adam Frankish (The Sanger Institute, HAVANA Group); Jennifer Harrow (The Sanger Institute, HAVANA Group); Gonzalo Lopez (CNIO, Structural Biology and Biocomputation); Nick Goldman (The European Bioinformatics Institute, The Goldman Group); Ari Loytynoja (The European Bioinformatics Institute, The Goldman Group); Tim Massingham (The European Bioinformatics Institute, The Goldman Group); Fabio Pardi (The European Bioinformatics Institute, The Goldman Group); Simon Whelan (University of Manchester, Faculty of Life Sciences);

Short Abstract: We have built an automatic pipeline to determine which alternative transcript is the principal functional variant for a gene. The pipeline detected principal variants for over 85% of the well-annotated genes in the ENCODE pilot project. The pipeline definitions were confirmed by the available experimental and transcript evidence.

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Poster I21

The Study of Pathways in Metagenomic Data by Transitive Association of Neighboring Genes

Iddo Friedberg- University of California San Deigo

John Wooley (UCSD, CALIT2); Weizhong Li (UCSD, CALIT2); Adam Godzik (UCSD, CALIT2); Paul Gilna (UCSD, CALIT2);

Short Abstract: We show that neighboring gene information in environmental shotgun sequence data can be used to reconstruct pathways, and to gauge the coverage of the metagenomic sample. We show examples of new evolutionary events in known pathways and introduce sentinel pathways that help us assess metagenomic sampling.

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Poster I22

Universal Seeds: Improving the Accuracy of Cross-Species cDNA-to-Genome Alignment

Liliana Florea- George Washington University

Leming Zhou (The George Washington University, Computer Science); Art Delcher (University of Maryland, Center for Bioinformatics and Computational Biology); Mihaela Pertea (University of Maryland, Center for Bioinformatics and Computational Biology);

Short Abstract: We develop methods and tools for accurate cross-species cDNA-to-genome alignment, to serve in the gene annotation of future genomes. Starting from mathematical models of alignment, we determine seeds that perform well on a wide range of comparisons at various evolutionary distances (universal seeds) and implement them into practical alignment tools.

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Poster I23

A Complete System for Community Genome Annotation

Scott Cain- Cold Spring Harbor Laboratory

Jim Hu (Texas A&M University, Biochemistry and Biophysics); Eric Just (Northwestern University, dictyBase); Brian O'Connor (University of California at Los Angeles, Human Genetics);

Short Abstract: Here we present a VMware virtual server with all of the software required preinstalled to facilitate community annotation of a sequenced genome. Components include GMOD software Chado, GBrowse, Apollo and GMODWeb, as well as MediaWiki with the TableEdit extension.

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