Genome-tools: a flexible package for genome sequence analysis

Genome-tools is a Perl module, a set of programs, and a user interface that facilitates access to genome sequence information. The package is flexible, extensible, and designed to be accessible and useful to both nonprogrammers and programmers. Any relatively well-annotated genome available with standard GenBank genome files may be used with genome-tools. A simple Web-based front end permits searching any available genome with an intuitive interface. Flexible design choices also make it simple to handle revised versions of genome annotation files as they change. In addition, programmers can develop cross-genomic tools and analyses with minimal additional overhead by combining genome-tools modules with newly written modules. Genome-tools runs on any computer platform for which Perl is available, including Unix, Microsoft Windows, and Mac OS. By simplifying the access to large amounts of genomic data, genome-tools may be especially useful for molecular biologists looking at newly sequenced genomes, for which few informatics tools are available. The genome-tools Web interface is accessible at http://genome-tools.sourceforge.net, and the source code is available at http://sourceforge.net/projects/genome-tools.     

Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms

Background  

Identifying syntenic regions, i.e., blocks of genes or other markers with evolutionary conserved order, and quantifying evolutionary relatedness between genomes in terms of chromosomal rearrangements is one of the central goals in comparative genomics. However, the analysis of synteny and the resulting assessment of genome rearrangements are sensitive to the choice of a number of arbitrary parameters that affect the detection of synteny blocks. In particular, the choice of a set of markers and the effect of different aggregation strategies, which enable coarse graining of synteny blocks and exclusion of micro-rearrangements, need to be assessed. Therefore, existing tools and resources that facilitate identification, visualization and analysis of synteny need to be further improved to provide a flexible platform for such analysis, especially in the context of multiple genomes.     

The Mycoplasma genome

A review is presented of the available data on the nature of chromosomal and extrachromosomal DNA of Mollicutes (mycoplasmas)--the smallest and simplest procaryotic organisms.     

The Icelandic genome debate

Three of the central issues in contemporary debates about the commodification of the human body are those of property, ownership, and access. This article uses the case of the central medical database on Icelanders to discuss contesting claims about the ownership of the human genome, with respect to the rapid development of biotechnology, human genome projects and DNA collections. We emphasize the contrast between commercial and communitarian perspectives and to illustrate our argument we explore debates about the Icelandic database. These debates have been intense, focusing on a range of issues, including ethics, academic freedom, public health and, last but not least, the control and ownership of medical records, genetic information and genealogical data. This article should be seen primarily as an anthropological commentary on ongoing developments.     

The genome sequence DataBase

The Genome Sequence DataBase (GSDB) is a database of publicly available nucleotide sequences and their associated biological and bibliographic information. Several notable changes have occurred in the past year: GSDB stopped accepting data submissions from researchers; ownership of data submitted to GSDB was transferred to GenBank; sequence analysis capabilities were expanded to include Smith-Waterman and Frame Search; and Sequence Viewer became available to Mac users. The content of GSDB remains up-to-date because publicly available data is acquired from the International Nucleotide Sequence Database Collaboration databases (IC) on a nightly basis. This allows GSDB to continue providing researchers with the ability to analyze, query and retrieve nucleotide sequences in the database. GSDB and its related tools are freely accessible from the URL: http://www.ncgr.org     

The ageing mitochondrial genome

The population of elderly individuals has increased significantly over the past century and is predicted to rise even more rapidly in the future. Ageing is a major risk factor for many diseases such as neurodegenerative disease, diabetes and cancer. This highlights the importance of understanding the mechanisms involved in the ageing process. One plausible mechanism for ageing is accumulation of mutations in the mitochondrial genome. In this review, we discuss some of the most convincing data surrounding age-related mtDNA mutations and the evidence that these mutations contribute to the ageing process.     

The cancer genome revealed

Human Cytogenetic Cancer Markersedited by Sandra R. Wolman and Stewart Sell, Humana Press, 1997. US $125.00 (xii+484 pages) ISBN 0 89603 357 0     

A biased detection of the flexible genome content: missing large restriction fragments in comparative genomics

Gene content variation between closely related bacteria is largely due to mobile elements and gene erosion. Various techniques are available to assess this variation, yet biased pools of restriction fragments have been used in several comparative genomics studies. Excluding important large restriction fragments from the actual hybridisation or from post-hybridisation amplification reactions compromise the comprehensiveness of these studies.     

The platypus genome unraveled

The genome of the platypus has been sequenced, assembled, and annotated by an international genomics team. Like the animal itself the platypus genome contains an amalgam of mammal, reptile, and bird-like features.     

The Rhodobacter capsulatus genome

The genome of Rhodobacter capsulatus has been completely sequenced. It consists of a single chromosome containing 3.5 Mb and a circular plasmid of 134 kb. This effort, started in 1992, began with a fine-structure restriction map of an overlapping set of cosmids that covered the genome. Cosmid sequencing led to a gapped genome that was filled by primer walking on the chromosome and by using lambda clones. Methods had to be developed to handle strong stops in the high GC (68%) inserts. Annotation was done with the ERGO system at Integrated Genomics, as was the reconstruction of the cell's metabolism. It was possible to recognize 3709 orfs of which functional assignments could be made with high confidence to 2392 (65%). Unusual features include the presence of numerous cryptic phage genomes embedded in the chromosome. This revised version was published online in June 2006 with corrections to the Cover Date.     

The evolving fungal genome

Fungal genomes vary considerably in size and organization. The genome of Microsporidium contains less than 3 Mb while the genomes of several Basidiomycetes and Ascomycetes greatly exceed 100 Mb. Likewise chromosome numbers and ploidy levels can differ even between closely related species. The differences in genome architecture among fungi reflect the interplay of different mutational processes as well as the population biology of the different species. Comparative genome studies have elucidated the underlying mechanisms of genome evolution in different groups of fungi and have provided insight into species-specific genomic traits. Mobile genetic elements have been instrumental in shaping the genome architecture and gene content in many fungal species. In many pathogenic fungi the mobile genetic elements even play a crucial role in rapid adaptive evolution by mediating high rates of sequence mutations, chromosomal rearrangements, and ploidy changes. But in many species mobile elements are efficiently restricted by defense mechanisms, which have evolved to suppress and regulate parasitic elements. Different rates of genome dynamic and adaptive evolution may reflect varying effective population sizes through which genetic drift and natural selection have differentially affected genome architecture in fungi over time.