BactPepDB: a database of predicted peptides from a exhaustive survey of complete prokaryote genomes.

With the recent progress in complete genome sequencing, mining the increasing amount of genomic information available should in theory provide the means to discover new classes of peptides. However, annotation pipelines often do not consider small reading frames likely to be expressed. BactPepDB, available online at http://bactpepdb.

GOHTAM: a website for 'Genomic Origin of Horizontal Transfers, Alignment and Metagenomics'.

Motivation: This website allows the detection of horizontal transfers based on a combination of parametric methods and proposes an origin by researching neighbors in a bank of genomic signatures. This bank is also used to research an origin to DNA fragments from metagenomics studies.

Results: Different services are provided like the possibility of inferring a phylogenetic tree with sequence signatures or comparing two genomes and displaying the rearrangements that happened since their separation.

The use of genomic signature distance between bacteriophages and their hosts displays evolutionary relationships and phage growth cycle determination.

Background: Bacteriophage classification is mainly based on morphological traits and genome characteristics combined with host information and in some cases on phage growth lifestyle. A lack of molecular tools can impede more precise studies on phylogenetic relationships or even a taxonomic classification. The use of methods to analyze genome sequences without the requirement for homology has allowed advances in classification.

A benchmark of parametric methods for horizontal transfers detection.

Horizontal gene transfer (HGT) has appeared to be of importance for prokaryotic species evolution. As a consequence numerous parametric methods, using only the information embedded in the genomes, have been designed to detect HGTs. Numerous reports of incongruencies in results of the different methods applied to the same genomes were published.

Whole genome evaluation of horizontal transfers in the pathogenic fungus Aspergillus fumigatus.

Background: Numerous cases of horizontal transfers (HTs) have been described for eukaryote genomes, but in contrast to prokaryote genomes, no whole genome evaluation of HTs has been carried out. This is mainly due to a lack of parametric methods specially designed to take the intrinsic heterogeneity of eukaryote genomes into account. We applied a simple and tested method based on local variations of genomic signatures to analyze the genome of the pathogenic fungus Aspergillus fumigatus.

Enhanced protein fold recognition using a structural alphabet.

Fold recognition from sequence can be an important step in protein structure and function prediction. Many methods have tackled this goal. Most of them, based on sequence alignment, fail for sequences of low similarity.

Horizontally acquired genomic islands in the tubercle bacilli.

Most mycobacteria are environmental species, causing disease only occasionally when they encounter a susceptible human or animal host. A few species, such as Mycobacterium tuberculosis and Mycobacterium avium, have acquired the ability to parasitize host macrophages during the course of evolution and have become major pathogens. Recent genetic studies in these two species have suggested that early episodes of horizontal transfer of genomic islands from surrounding environmental species might have contributed to the evolution towards this virulence phenotype, possibly by helping bacilli to persist in protozoa and, subsequently, in mammalian phagocytes.

Contribution of horizontally acquired genomic islands to the evolution of the tubercle bacilli.

The contribution of horizontal gene transfer (HGT) to the evolution of Mycobacterium tuberculosis -- the main causal agent of tuberculosis in humans -- and closely related members of the M. tuberculosis complex remains poorly understood. Using a combination of genome-wide parametric analyses, we have identified 48 M.

Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome.

We report results of a megabase-scale phylogenomic analysis of the Reptilia, the sister group of mammals. Large-scale end-sequence scanning of genomic clones of a turtle, alligator, and lizard reveals diverse, mammal-like landscapes of retroelements and simple sequence repeats (SSRs) not found in the chicken. Several global genomic traits, including distinctive phylogenetic lineages of CR1-like long interspersed elements (LINEs) and a paucity of A-T rich SSRs, characterize turtles and archosaur genomes, whereas higher frequencies of tandem repeats and a lower global GC content reveal mammal-like features in Anolis.

Horizontal transfer of a virulence operon to the ancestor of Mycobacterium tuberculosis.

The contribution of interspecies horizontal gene transfer (HGT) to the evolution and virulence of Mycobacterium tuberculosis, the agent of tuberculosis in humans, has been barely investigated. Here we have studied the evolutionary history of the M. tuberculosis Rv0986-8 virulence operon recently identified, through functional genomics approaches, as playing an important role in parasitism of host phagocytic cells.

Exploration of phylogenetic data using a global sequence analysis method.

Background: Molecular phylogenetic methods are based on alignments of nucleic or peptidic sequences. The tremendous increase in molecular data permits phylogenetic analyses of very long sequences and of many species, but also requires methods to help manage large datasets.

Results: Here we explore the phylogenetic signal present in molecular data by genomic signatures, defined as the set of frequencies of short oligonucleotides present in DNA sequences.

Indications for acquisition of reductive dehalogenase genes through horizontal gene transfer by Dehalococcoides ethenogenes strain 195.

The genome of Dehalococcoides ethenogenes strain 195, an anaerobic dehalorespiring bacterium, contains 18 copies of putative reductive dehalogenase genes, including the well-characterized tceA gene, whose gene product functions as the key enzyme in the environmentally important dehalorespiration process. The genome of D. ethenogenes was analyzed using a bioinformatic tool based on the frequency of oligonucleotides.

Detection and characterization of horizontal transfers in prokaryotes using genomic signature.

Horizontal DNA transfer is an important factor of evolution and participates in biological diversity. Unfortunately, the location and length of horizontal transfers (HTs) are known for very few species. The usage of short oligonucleotides in a sequence (the so-called genomic signature) has been shown to be species-specific even in DNA fragments as short as 1 kb.

A genomic schism in birds revealed by phylogenetic analysis of DNA strings.

The molecular systematics of vertebrates has been based entirely on alignments of primary structures of macromolecules; however, higher order features of DNA sequences not used in traditional studies also contain valuable phylogenetic information. Recent molecular data sets conflict over the phylogenetic placement of flightless birds (ratites - paleognaths), but placement of this clade critically influences interpretation of character change in birds. To help resolve this issue, we applied a new bioinformatics approach to the largest molecular data set currently available.