G-compass: A web-based comparative genome browser between human and other vertebrate genomes

for 15 vertebrate, insect and other animal species; (iii) it provides comprehensive comparative genomics information for comparing alternative splicing and splice site conservation across 17 aligned genomes, based on UCSC multigenome alignments; (iv) it provides an 2- to 3-fold expansion in detection

Major histocompatibility complex (MHC) genes play a critical role in vertebrate immune response and because the MHC is linked to a significant number of auto-immune and other diseases it is of great medical interest. Here we describe the clone-based sequencing and subsequent annotation of the MHC

in the genomes of almost all vertebrates examined, from humans and other mammals to most teleost fish. However, ZIP12 appears to be absent from the zebrafish genome. The discrimination of ZIP12 compared to ZIP4 was unsuccessful or inconclusive in other invertebrate chordates and deuterostomes. Splice variation

in humans: the natural killer complex on Chromosome 12p13.1, which encodes C-type lectin molecules, and the leukocyte receptor complex on Chromosome 19q13.4, which encodes immunoglobulin superfamily molecules. The composition of these gene clusters differs markedly between closely related species, providing

and comparative links between the two species are being 1994). Groups containing species with ongoing or prospective genome sequencing projects are indicated (solid and dashed lined boxes, respectively). The tree is calibrated according to the fossil record (based on Another example was data analysis; many

biologists who wish to develop or use ontologies. In the main ISMB conference, the use of semantic web, or at least its technologies, was a recurrent theme. A recurrent issue in this year's meeting, highlighted particularly by Mark Musen's keynote, are the attempts to move bio-ontology development

-quality genomes and associated transcriptomes to carry out a detailed examination of HGT in 26 animal species (10 primates, 12 flies and four nematodes) and a simplified analysis in a further 14 vertebrates. Genome-wide comparative and phylogenetic analyses show that HGT in animals typically gives rise to tens

, and a web-based front end, which offers a biologically centered interface to browse, visualize, and compare different data sets. Download and Installation instructions, user's manual, discussion group, and a prototype are available at http://expressionplot.com/. Main Text RNA-Seq has emerged

genomes, the elephant shark genome has not experienced an additional wholegenome duplication. These findings underscore the importance of the elephant shark as a critical reference vertebrate genome for comparative analysis of the human and other vertebrate genomes. This study also demonstrates that a