Originoflife. The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. + Author Affiliations * To whom correspondence should be addressed.
Received June 5, 2009. Revision received July 21, 2009. Accepted July 30, 2009. Summary: Experimental techniques that survey an entire genome demand flexible, highly interactive visualization tools that can display new data alongside foundation datasets, such as reference gene annotations. Availability: The application and source code are available from and. Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content.
OrthoClusterDB: an online platform for synteny blocks. Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes. + Author Affiliations *To whom correspondence should be addressed.
Measure of synonymous codon usage diversity among genes in bacteria. How to find simple and accurate rules for viral protease cleavage specificities. Data HIV-1 protease data You et al. [15] collected a HIV-1 protease substrate data set containing 746 octamers, of which 401 are cleaved and 345 are non-cleaved.
In this data set, the octamer SQNYAIVQ was originally erroneously labeled as non-cleaved [16]. This error was corrected and the resulting data set is referred to as the HIV-1 PR 746 data set in this study. CodonExplorer: an online tool for analyzing codon usage and sequence composition, scaling from genes to genomes. Visualization of genomic data with the Hilbert curve. Simon Anders + Author Affiliations.
An archaeal Rad54 protein remodels DNA and stimulates DNA strand exchange by RadA. + Author Affiliations *To whom correspondence should be addressed.
Tel: +1 530 752 5938; Fax: +1 530 752 5939; Email: sckowalczykowski@ucdavis.edu Received November 2, 2008. Revision received January 22, 2009. Accepted January 22, 2009. Rad54 protein is a key member of the RAD52 epistasis group required for homologous recombination in eukaryotes. Oxidative stress induces degradation of mitochondrial DNA. + Author Affiliations *To whom correspondence should be addressed.
Tel: +1 251 460 6789; Fax: +1 251 460 6771; Email: malexeye@jaguar1.usouthal.edu Received September 4, 2008. Revision received January 25, 2009. A novel zinc-binding fold in the helicase interaction domain of the Bacillus subtilis DnaI helicase loader. + Author Affiliations *To whom correspondence should be addressed.
Tel: +371 6701 4817; Fax: +371 6755 0338; Email: edv@osi.lv Received December 18, 2008. Revision received January 15, 2009. Accepted February 2, 2009. The helicase loader protein DnaI (the Bacillus subtilis homologue of Escherichia coli DnaC) is required to load the hexameric helicase DnaC (the B. subtilis homologue of E. coli DnaB) onto DNA at the start of replication. Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2. + Author Affiliations *To whom correspondence should be addressed.
Tel: +1 416 946 3868; Fax: +1 416 946 0588; Email: jr.min@utoronto.ca Received December 2, 2008. Revision received January 9, 2009. Accepted January 30, 2009. The MBT repeat has been recently identified as a key domain capable of methyl–lysine histone recognition. . © 2009 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Integration of phenotypic metadata and protein similarity in Archaea using a spectral bipartitioning approach. + Author Affiliations *To whom correspondence should be addressed.
Email: SHooper@lbl.gov Received October 7, 2008. Revision received January 6, 2009. Accepted January 27, 2009. In order to simplify and meaningfully categorize large sets of protein sequence data, it is commonplace to cluster proteins based on the similarity of those sequences. . © 2009 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
The human GINS complex associates with Cdc45 and MCM and is essential for DNA replication. + Author Affiliations *To whom correspondence should be addressed. Tel: +34 91 732 8000 (ext. 3490); Fax: +34 91 732 8033; Email: jmendez@cnio.es Received December 27, 2008. Revision received January 23, 2009. Accepted January 24, 2009. The GINS complex, originally discovered in Saccharomyces cerevisiae and Xenopus laevis, binds to DNA replication origins shortly before the onset of S phase and travels with the replication forks after initiation. A multiple sequence alignment editor and analysis workbench. + Author Affiliations *To whom correspondence should be addressed.
Received November 24, 2008. Revision received November 24, 2008. Accepted January 8, 2009. The Effect of Sequence Evolution on Protein Structural Divergence. The complex constraints imposed by protein structure and function result in varied rates of sequence and structural divergence in proteins. Analysis of sequence differences between homologous proteins can advance our understanding of structural divergence and some of the constraints that govern the evolution of these molecules. Here, we assess the relationship between amino acid sequence and structural divergence.
Firstly, we demonstrate that the relationship between protein sequence and structural divergence is governed by a variety of evolutionary constraints, including solvent exposure and secondary structure. Secondly, although compensatory substitutions are widespread, we find many radical size-changing mutations that are not compensated by neighboring complementary changes. Phylogenetic Signals in DNA Composition: Limitations and Prospects.
Jan Mrázek + Author Affiliations E-mail: mrazek@uga.edu. Accepted February 16, 2009. The concept of genome signature allows sequence comparisons without alignment. It relies on the premise that oligonucleotide compositions of DNA segments from the same or closely related genomes tend to be more similar than those from distantly related genomes. The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota. A web-based software system for dynamic gene cluster comparison across multiple genomes. CGAS: comparative genomic analysis server. Fart molecule could be next Viagra - health - 06 March 2009. THE stink of flatulence and rotten eggs could provide a surprising lift for men.
Hydrogen sulphide (H2S) causes erections in rats and may one day provide an alternative to Viagra for men. The penis is packed with spongy tissue that produces an erection when it fills with blood. Nitric oxide (NO) helps relax the walls of arteries that supply the penis, allowing extra blood to flow in. Finding 3D motifs in ribosomal RNA structures. IslandViewer: an integrated interface for computational identification and visualization of genomic islands. AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context.
Host-parasite relations of bacteria and phages can be unveiled by Oligostickiness, a measure of relaxed sequence similarity. A versatile non-radioactive assay for DNA methyltransferase activity and DNA binding. Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms. CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome? CGIs versus CGCs: statistics in the human and mouse genomes Table 1 shows the statistics of CGIs by Takai and Jones' algorithm and CGCs by CpGcluster in the human and mouse genomes.
The number of CGCs is remarkably larger than that of CGIs. In the human genome, there are 198,702 CGCs, 5.3 times the number of CGIs (37,729). Similarly, in the mouse genome, the number of CGCs (121,885) is 5.7 times that of CGIs (21,326). Inferring Selection on Amino Acid Preference in Protein Domains. Escherichia coli genes affecting recipient ability in plasmid conjugation: Are there any? Two unique membrane-bound AAA proteins from Sulfol...[Biochem Soc Trans. 2009] - PubMed Result.
Conditions for gene disruption by homologous recom...[Archaea. 2008] - PubMed Result. Proteomic characterization of the sulfur-reducing ...[Extremophiles. 2009] - PubMed Result. Studies on the base excision repair (BER) complex ...[Biochem Soc Trans. 2009] - PubMed Result. Atomic structures and functional implications of t...[BMC Struct Biol. 2009] - PubMed Result. Genome and gene alterations by insertions and deletions in the evolution of human and chimpanzee chromosome 22.
Identification and analysis of indels We identified 6,278 indels (≥ 10 bp) in a comparison between 33 Mb of syntenic regions from human and chimpanzee chromosome 22, using human genome as a reference (Fig. S1(see Additional file 1)). Human sequence extended from 15.4 to 49.3 Mb while the chimpanzee sequence covered a region from 15.4 to 50.0 Mb (Table 1).
Most of these variants were found around simple sequence repeats (2,572), but similar numbers were located in and around the known repetitive DNA sequences (2,277) and were filtered out (Table 1). For simplicity, throughout this paper we refer to the data set containing the remaining 1,429 repeat-filtered sequences as the "observed" dataset. Large-scale inference of the point mutational spectrum in human segmental duplications. Expression profiles and physiological roles of two...[Appl Environ Microbiol. 2008] - PubMed Result. Une expérience d'ensemencement en fer de l'océan dans l'Atlantique Sud - Planète - Le Monde.fr. LE MONDE | • Mis à jour le | Par Hervé Kempf Le polarstern ("l'étoile polaire") vogue vers les 40es rugissants. Parti mercredi 7 janvier du Cap, en Afrique du Sud, il doit atteindre une zone située dans l'Atlantique sud, par 50° S de latitude et 37° W de longitude.
Le bateau de l'institut de recherche allemand Alfred-Wegener ne navigue pas dans les mêmes eaux que ceux du Vendée Globe : sa mission est de voir si l'ensemencement de l'océan en fer pourrait limiter le changement climatique. L'expérience, baptisée Lahofex et menée en coopération avec l'Institut national d'océanographie d'Inde, consiste à répandre environ 20 tonnes de fer sur 300 km2 d'océan. "Dans cette zone, la mer est pauvre en fer, ce qui limite le développement du phytoplancton, explique Lars Stemmann, du laboratoire d'océanographie de Villefranche-sur-Mer (Alpes-Maritimes), scientifique français impliqué dans l'expérience.
Le fait que du plancton se développe en cas d'apport de fer est déjà bien établi. Actualité > Le poisson abyssal qui a inventé le télescope... GenomeGraphs: integrated genomic data visualization with R. Generation, Biological Consequences and Repair Mec...[J Radiat Res (Tokyo). 2008] - PubMed Result. Complete genome sequence of the anaerobic, protein...[J Bacteriol. 2008] - PubMed Result. Actualité > Des bactéries qui carburent à l'eau irradiée !
Feature selection environment for genomic applications.