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.

The DNA sequence and analysis of human chromosome 13.

Chromosome 13 is the largest acrocentric human chromosome. It carries genes involved in cancer including the breast cancer type 2 (BRCA2) and retinoblastoma (RB1) genes, is frequently rearranged in B-cell chronic lymphocytic leukaemia, and contains the DAOA locus associated with bipolar disorder and schizophrenia. We describe completion and analysis of 95.5 megabases (Mb) of sequence from chromosome 13, which contains 633 genes and 296 pseudogenes. We estimate that more than 95.4% of the protein-coding genes of this chromosome have been identified, on the basis of comparison with other vertebrate genome sequences. Additionally, 105 putative non-coding RNA genes were found. Chromosome 13 has one of the lowest gene densities (6.5 genes per Mb) among human chromosomes, and contains a central region of 38 Mb where the gene density drops to only 3.1 genes per Mb.

Ensembl 2004.

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organize biology around the sequences of large genomes. It is a comprehensive and integrated source of annotation of large genome sequences, available via interactive website, web services or flat files. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. The facilities of the system range from sequence analysis to data storage and visualization and installations exist around the world both in companies and at academic sites. With a total of nine genome sequences available from Ensembl and more genomes to follow, recent developments have focused mainly on closer integration between genomes and external data.

The DNA sequence and analysis of human chromosome 6.

Chromosome 6 is a metacentric chromosome that constitutes about 6% of the human genome. The finished sequence comprises 166,880,988 base pairs, representing the largest chromosome sequenced so far. The entire sequence has been subjected to high-quality manual annotation, resulting in the evidence-supported identification of 1,557 genes and 633 pseudogenes. Here we report that at least 96% of the protein-coding genes have been identified, as assessed by multi-species comparative sequence analysis, and provide evidence for the presence of further, otherwise unsupported exons/genes. Among these are genes directly implicated in cancer, schizophrenia, autoimmunity and many other diseases. Chromosome 6 harbours the largest transfer RNA gene cluster in the genome; we show that this cluster co-localizes with a region of high transcriptional activity. Within the essential immune loci of the major histocompatibility complex, we find HLA-B to be the most polymorphic gene on chromosome 6 and in the human genome.

Ensembl 2002: accommodating comparative genomics.

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of human, mouse and other genome sequences, available as either an interactive web site or as flat files. Ensembl also integrates manually annotated gene structures from external sources where available. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. These range from sequence analysis to data storage and visualisation and installations exist around the world in both companies and at academic sites. With both human and mouse genome sequences available and more vertebrate sequences to follow, many of the recent developments in Ensembl have focusing on developing automatic comparative genome analysis and visualisation.

The Ensembl genome database project.

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources, and is available as either an interactive web site or as flat files. It is also an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements from sequence analysis to data storage and visualisation. The Ensembl site is one of the leading sources of human genome sequence annotation and provided much of the analysis for publication by the international human genome project of the draft genome. The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops.

Apollo: a sequence annotation editor.

The well-established inaccuracy of purely computational methods for annotating genome sequences necessitates an interactive tool to allow biological experts to refine these approximations by viewing and independently evaluating the data supporting each annotation. Apollo was developed to meet this need, enabling curators to inspect genome annotations closely and edit them. FlyBase biologists successfully used Apollo to annotate the Drosophila melanogaster genome and it is increasingly being used as a starting point for the development of customized annotation editing tools for other genome projects.

Mining the draft human genome.

Now that the draft human genome sequence is available, everyone wants to be able to use it. However, we have perhaps become complacent about our ability to turn new genomes into lists of genes. The higher volume of data associated with a larger genome is accompanied by a much greater increase in complexity. We need to appreciate both the scale of the challenge of vertebrate genome analysis and the limitations of current gene prediction methods and understanding.

The DNA sequence and comparative analysis of human chromosome 20.

The finished sequence of human chromosome 20 comprises 59,187,298 base pairs (bp) and represents 99.4% of the euchromatic DNA. A single contig of 26 megabases (Mb) spans the entire short arm, and five contigs separated by gaps totalling 320 kb span the long arm of this metacentric chromosome. An additional 234,339 bp of sequence has been determined within the pericentromeric region of the long arm. We annotated 727 genes and 168 pseudogenes in the sequence. About 64% of these genes have a 5' and a 3' untranslated region and a complete open reading frame. Comparative analysis of the sequence of chromosome 20 to whole-genome shotgun-sequence data of two other vertebrates, the mouse Mus musculus and the puffer fish Tetraodon nigroviridis, provides an independent measure of the efficiency of gene annotation, and indicates that this analysis may account for more than 95% of all coding exons and almost all genes.

ProtEST: protein multiple sequence alignments from expressed sequence tags.

MOTIVATION: An automatic sequence searching method (ProtEST) is described which constructs multiple protein sequence alignments from protein sequences and translated expressed sequence tags (ESTs). ProtEST is more effective than a simple TBLASTN search of the query against the EST database, as the sequences are automatically clustered, assembled, made non-redundant, checked for sequence errors, translated into protein and then aligned and displayed. RESULTS: A ProtEST search found a non-redundant, translated, error- and length-corrected EST sequence for > 58% of sequences when single sequences from 1407 Pfam-A seed alignments were used as the probe. The average family size of the resulting alignments of translated EST sequences contained > 10 sequences. In a cross-validated test of protein secondary structure prediction, alignments from the new procedure led to an improvement of 3.4% average Q3 prediction accuracy over single sequences. AVAILABILITY: The ProtEST method is available as an Internet World Wide Web service http://barton.ebi.ac.uk/servers/protest.html+ ++ The Wise2 package for protein and genomic comparisons and the ProtESTWise script can be found at http://www.sanger.ac.uk/Software/Wise2 CONTACT: geoff@ebi.ac.uk

The DNA sequence of human chromosome 22.

Knowledge of the complete genomic DNA sequence of an organism allows a systematic approach to defining its genetic components. The genomic sequence provides access to the complete structures of all genes, including those without known function, their control elements, and, by inference, the proteins they encode, as well as all other biologically important sequences. Furthermore, the sequence is a rich and permanent source of information for the design of further biological studies of the organism and for the study of evolution through cross-species sequence comparison. The power of this approach has been amply demonstrated by the determination of the sequences of a number of microbial and model organisms. The next step is to obtain the complete sequence of the entire human genome. Here we report the sequence of the euchromatic part of human chromosome 22. The sequence obtained consists of 12 contiguous segments spanning 33.4 megabases, contains at least 545 genes and 134 pseudogenes, and provides the first view of the complex chromosomal landscapes that will be found in the rest of the genome.

A randomised controlled trial of general practitioner safety advice for families with children under 5 years.

OBJECTIVE: To assess effectiveness of general practitioner advice about child safety, and provision of low cost safety equipment to low income families, on use of safety equipment and safe practices at home. DESIGN: Randomised, unblinded, controlled trial with initial assessment and six week follow up by telephone survey. Twenty families from intervention and control groups were randomly selected for a home visit to assess validity of responses to second survey. SETTING: A general practice in Nottingham. SUBJECTS: 98% (165/169) of families with children aged under 5 years registered with the practice. INTERVENTIONS: General practitioner safety advice plus, for families receiving means tested state benefits, access to safety equipment at low cost. Control families received usual care. MAIN OUTCOME MEASURES: Possession and use of safety equipment and safe practices at home. RESULTS: Before intervention, the two groups differed only in possession of fireguards. After intervention, significantly more families in intervention group used fireguards (relative risk 1.89, 95% confidence interval 1.18 to 2.94), smoke alarms (1.14, 1.04 to 1.25), socket covers (1.27, 1.10 to 1.48), locks on cupboards for storing cleaning materials (1.38, 1.02 to 1.88), and door slam devices (3.60, 2.17 to 5.97). Also, significantly more families in intervention group showed very safe practice in storage of sharp objects (1.98, 1.38 to 2.83), storage of medicines (1.15, 1.03 to 1.28), window safety (1.30, 1.06 to 1.58), fireplace safety (1.84, 1.34 to 2.54), socket safety (1.77, 1.37 to 2.28), smoke alarm safety (1.11, 1.01 to 1.22), and door slam safety (7.00, 3.15 to 15.6). Stratifying results by receipt of state benefits showed that intervention was at least as effective in families receiving benefits as others. CONCLUSIONS: General practitioner advice, coupled with access to low cost equipment for low income families, increased use of safety equipment and other safe practices. These findings are encouraging for provision of injury prevention in primary care.

JPred: a consensus secondary structure prediction server.

UNLABELLED: An interactive protein secondary structure prediction Internet server is presented. The server allows a single sequence or multiple alignment to be submitted, and returns predictions from six secondary structure prediction algorithms that exploit evolutionary information from multiple sequences. A consensus prediction is also returned which improves the average Q3 accuracy of prediction by 1% to 72.9%. The server simplifies the use of current prediction algorithms and allows conservation patterns important to structure and function to be identified. AVAILABILITY: http://barton.ebi.ac.uk/servers/jpred.h tml CONTACT: geoff@ebi.ac.uk

Comparative trial of nifedipine retard and atenolol in the treatment of elderly patients with mild to moderate hypertension.

Forty-one elderly patients with mild to moderate hypertension (resting diastolic blood pressure 100-130 mmHg after an eight week placebo run-in phase) were randomised to a double-blind parallel group comparison of nifedipine retard 10 mg twice daily or atenolol 50 mg once daily. If the resting diastolic pressure exceeded 95 mmHg after four weeks of treatment the dose(s) were doubled for a further four weeks. Initial sitting blood pressures were 187 +/- 21/105 +/- 5 mmHg in the nifedipine group and 181 +/- 19/106 +/- 6 in the atenolol group. At four weeks, eight patients given nifedipine and nine given atenolol had their doses doubled. At eight weeks sitting blood pressures were 159 +/- 19/85 +/- 7 and 162 +/- 21/87 +/- 8 respectively, with 18/20 patients given nifedipine and 16/21 given atenolol having a sitting diastolic pressure equal to or less than 95 mmHg. One patient given nifedipine was withdrawn because of unacceptable ankle oedema and one given atenolol withdrawn because of worsening angina. Both drugs were equally acceptable to the patients and neither caused a change in their sense of well-being.

Can audit improve patient care? Effects of studying use of digoxin in general practice.

A survey of monitoring of digoxin treatment in five practices examined the indications for prescribing digoxin, its long term use, and how its use could be monitored. These data were used to generate a protocol for monitoring treatment with digoxin in general practice. The findings of the survey and the protocol were distributed to and discussed with all the partners in the practices participating in the study. One year later similar analysis showed that record keeping (recording of pulse rate and rhythm) had improved significantly in the group of principals carrying out the audit but not in other principals in these practices. Audit may change only the auditors.