Paralog analyses reveal gene duplication events and genes under positive selection in Ixodes scapularis and other ixodid ticks.

Background: Hard ticks (family Ixodidae) are obligatory hematophagous ectoparasites of worldwide medical and veterinary importance. The haploid genomes of multiple species of ixodid ticks exceed 1 Gbp, prompting questions regarding gene, segmental and whole genome duplication in this phyletic group. The availability of the genome assembly for the black legged tick, Ixodes scapularis, and transcriptome datasets for multiple species of ticks offers an opportunity to assess the contribution of gene duplication to the genome.

Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing.

Background: Soybean, Glycine max (L.) Merr., is a well documented paleopolyploid.

xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features.

The eXtensible Genome Data Broker (xGDB) provides a software infrastructure consisting of integrated tools for the storage, display, and analysis of genome features in their genomic context. Common features include gene structure annotations, spliced alignments, mapping of repetitive sequence, and microarray probes, but the software supports inclusion of any property that can be associated with a genomic location. The xGDB distribution and user support utilities are available online at the xGDB project website, http://xgdb.

Sequence conservation of homeologous bacterial artificial chromosomes and transcription of homeologous genes in soybean (Glycine max L. Merr.).

The paleopolyploid soybean genome was investigated by sequencing homeologous BAC clones anchored by duplicate N-hydroxycinnamoyl/benzoyltransferase (HCBT) genes. The homeologous BACs were genetically mapped to linkage groups C1 and C2. Annotation of the 173,747- and 98,760-bp BACs showed that gene conservation in both order and orientation is high between homeologous regions with only a single gene insertion/deletion and local tandem duplications differing between the regions.

yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes.

Your Gene structure Annotation Tool for Eukaryotes (yrGATE) provides an Annotation Tool and Community Utilities for worldwide web-based community genome and gene annotation. Annotators can evaluate gene structure evidence derived from multiple sources to create gene structure annotations. Administrators regulate the acceptance of annotations into published gene sets.

Comparative plant genomics resources at PlantGDB.

PlantGDB (http://www.plantgdb.org/) is a database of plant molecular sequences.

Community-based gene structure annotation.

Uncertainty and inconsistency of gene structure annotation remain limitations on research in the genome era, frustrating both biologists and bioinformaticians, who have to sort out annotation errors for their genes of interest or to generate trustworthy datasets for algorithmic development. It is unrealistic to hope for better software solutions in the near future that would solve all the problems. The issue is all the more urgent with more species being sequenced and analyzed by comparative genomics - erroneous annotations could easily propagate, whereas correct annotations in one species will greatly facilitate annotation of novel genomes.

PlantGDB, plant genome database and analysis tools.

PlantGDB (http://www.plantgdb.org/) is a database of molecular sequence data for all plant species with significant sequencing efforts.

GeneSeqer@PlantGDB: Gene structure prediction in plant genomes.

The GeneSeqer@PlantGDB Web server (http://www.plantgdb.org/cgi-bin/GeneSeqer.

Refined annotation of the Arabidopsis genome by complete expressed sequence tag mapping.

Expressed sequence tags (ESTs) currently encompass more entries in the public databases than any other form of sequence data. Thus, EST data sets provide a vast resource for gene identification and expression profiling. We have mapped the complete set of 176,915 publicly available Arabidopsis EST sequences onto the Arabidopsis genome using GeneSeqer, a spliced alignment program incorporating sequence similarity and splice site scoring.

Hurricane Georges: a cross-national study examining preparedness, resource loss, and psychological distress in the U.S. Virgin Islands, Puerto Rico, Dominican Republic, and the United States.

This cross-national study examined preparation for and psychological functioning following Hurricane Georges in the U.S. Virgin Islands, Puerto Rico, Dominican Republic, and the United States.