The Vertebrate Genome Annotation (Vega) database

The Vertebrate Genome Annotation (Vega) database (http://vega.sanger.ac.uk) has been designed to be a community resource for browsing manual annotation of finished sequences from a variety of vertebrate genomes. Its core database is based on an Ensembl-style schema, extended to incorporate curation-specific metadata. In collaboration with the genome sequencing centres, Vega attempts to present consistent high-quality annotation of the published human chromosome sequences. In addition, it is also possible to view various finished regions from other vertebrates, including mouse and zebrafish. Vega displays only manually annotated gene structures built using transcriptional evidence, which can be examined in the browser. Attempts have been made to standardize the annotation procedure across each vertebrate genome, which should aid comparative analysis of orthologues across the different finished regions

Ensembl 2005

The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased by 7 to 16, with the addition of the six vertebrate genomes of chimpanzee, dog, cow, chicken, tetraodon and frog and the insect genome of honeybee. The majority have been annotated automatically using the Ensembl gene build system, showing its flexibility to reliably annotate a wide variety of genomes. With the increased number of vertebrate genomes, the comparative analysis provided to users has been greatly improved, with new website interfaces allowing annotation of different genomes to be directly compared. The Ensembl software system is being increasingly widely reused in different projects showing the benefits of a completely open approach to software development and distribution

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Codon bias in the ß-lactam procucer Acremonium chrysogenum

In this paper we compile the G/C-content, the codon bias, and consensus sequences for the translation initiation and the intron splicing sites from 19 nuclear genes of the major ß-lactam antibiotic producer Acremonium chrysogenum. Our data are compared with those from other filamentous fungi, such as Aspergillus nidulan, Neurospora crassa, and Sordaria macrospora

Vibratory and Acoustical Factors in Multimodal Reproduction of Concert DVDs

Abstract. Sound and vibration perception are always coupled in live music experience. Just think of a rock concert or hearing (and feeling) a church organ sitting on a wooden pew. Even in classical concerts kettle-drum and double bass are sensed not only with our ears. The air-borne sound causes seat vibrations or excites the skin surface directly. For some instruments (e.g. an organ) structure-borne sound is transmitted directly from the instrument to the listener. If concert recordings are played back with multimedia hi-fi systems at home, these vibratory information is missing in the majority of cases. This is due to low reproduction levels or to the limited frequency range of conventional loudspeakers. The audio signal on todays DVDs contains an additional channel for low frequency effects (LFE), which is intended for reproduction using a subwoofer. The generation of tactile components is still very restricted. An enhancement of such a systems might be possible using an electrodynamical shaker which generates whole body vibration (WBV) for a seated person. This paper describes a system implementing this approach. The genera-tion of a vibrotactile signal from the existing audio channels is analyzed. Different parameters during this process (amplitude of the vibration, fre-quency range) are examined in relation to their perceptual consequences using psychophysical experiments