AnnoTrack - a tracking system for genome annotation

<p>Abstract</p> <p>Background</p> <p>As genome sequences are determined for increasing numbers of model organisms, demand has grown for better tools to facilitate unified genome annotation efforts by communities of biologists. Typically this process involves numerous experts from the field and the use of data from dispersed sources as evidence. This kind of collaborative annotation project requires specialized software solutions for efficient data tracking and processing.</p> <p>Results</p> <p>As part of the scale-up phase of the ENCODE project (Encyclopedia of DNA Elements), the aim of the GENCODE project is to produce a highly accurate evidence-based reference gene annotation for the human genome. The <it>AnnoTrack </it>software system was developed to aid this effort. It integrates data from multiple distributed sources, highlights conflicts and facilitates the quick identification, prioritisation and resolution of problems during the process of genome annotation.</p> <p>Conclusions</p> <p>AnnoTrack has been in use for the last year and has proven a very valuable tool for large-scale genome annotation. Designed to interface with standard bioinformatics components, such as DAS servers and Ensembl databases, it is easy to setup and configure for different genome projects. The source code is available at <url>http://annotrack.sanger.ac.uk</url>.</p

Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates

Novel human pseudogenes are identified that had previous functionality and their age is estimated. The rate of loss-of-function occurred uniformly

Identifying protein-coding genes in genomic sequences

A review of the main computational pipelines used to generate the human reference protein-coding gene sets

The tammar wallaby major histocompatibility complex shows evidence of past genomic instability

BACKGROUND The major histocompatibility complex (MHC) is a group of genes with a variety of roles in the innate and adaptive immune responses. MHC genes form a genetically linked cluster in eutherian mammals, an organization that is thought to confer functional and evolutionary advantages to the immune system. The tammar wallaby (Macropus eugenii), an Australian marsupial, provides a unique model for understanding MHC gene evolution, as many of its antigen presenting genes are not linked to the MHC, but are scattered around the genome. RESULTS Here we describe the 'core' tammar wallaby MHC region on chromosome 2q by ordering and sequencing 33 BAC clones, covering over 4.5 MB and containing 129 genes. When compared to the MHC region of the South American opossum, eutherian mammals and non-mammals, the wallaby MHC has a novel gene organization. The wallaby has undergone an expansion of MHC class II genes, which are separated into two clusters by the class III genes. The antigen processing genes have undergone duplication, resulting in two copies of TAP1 and three copies of TAP2. Notably, Kangaroo Endogenous Retroviral Elements are present within the region and may have contributed to the genomic instability. CONCLUSIONS The wallaby MHC has been extensively remodeled since the American and Australian marsupials last shared a common ancestor. The instability is characterized by the movement of antigen presenting genes away from the core MHC, most likely via the presence and activity of retroviral elements. We propose that the movement of class II genes away from the ancestral class II region has allowed this gene family to expand and diversify in the wallaby. The duplication of TAP genes in the wallaby MHC makes this species a unique model organism for studying the relationship between MHC gene organization and function.This work was funded by an ARC Discovery Grant to KB and SB, and a Wellcome Trust Grant (084071) to SB. HVS was supported by a University of Sydney Postgraduate Award and a William and Catherine McIlrath Scholarship for travel to the Sanger Institute. JK and HVS are supported in part by Wellcome Trust Programme grant 089305. KB is supported by a University of Sydney Thompson fellowship and an ARC Future Fellowship

A practical scheme for quantum computation with any two-qubit entangling gate

Which gates are universal for quantum computation? Although it is well known that certain gates on two-level quantum systems (qubits), such as the controlled-not (CNOT), are universal when assisted by arbitrary one-qubit gates, it has only recently become clear precisely what class of two-qubit gates is universal in this sense. Here we present an elementary proof that any entangling two-qubit gate is universal for quantum computation, when assisted by one-qubit gates. A proof of this important result for systems of arbitrary finite dimension has been provided by J. L. and R. Brylinski [arXiv:quant-ph/0108062, 2001]; however, their proof relies upon a long argument using advanced mathematics. In contrast, our proof provides a simple constructive procedure which is close to optimal and experimentally practical [C. M. Dawson and A. Gilchrist, online implementation of the procedure described herein (2002), http://www.physics.uq.edu.au/gqc/].Comment: 3 pages, online implementation of procedure described can be found at http://www.physics.uq.edu.au/gqc

Lessons learned from the initial sequencing of the pig genome: comparative analysis of an 8 Mb region of pig chromosome 17

The sequencing, annotation and comparative analysis of an 8Mb region of pig chromosome 17 allows the coverage and quality of the pig genome sequencing project to be assesse