Meta-analysis to test the association of HIV-1 nef with disease progression

Pushker et al. (2010) Journal of Virology

Previous relatively small studies have associated particular amino acid replacements and deletions in the HIV-1 nef gene with differences in the rate of HIV disease progression. We tested more rigorously whether particular nef amino acid differences and deletions are associated with HIV disease progression. Amino acid replacements and deletions in patients' consensus sequences were investigated for 153 progressor (P), 615 long-term nonprogressor (LTNP), and 2,311 unknown progressor sequences from 582 subtype B HIV-infected patients. [More]

The Neolithic revolution of bacterial genomes

Mira et al. (2006) Trends in Microbiology

Current human activities undoubtedly impact natural ecosystems. However, the influence of Homo sapiens on living organisms must have also occurred in the past. We show that certain genomic characteristics of prokaryotes can be used to study the impact of ancient human activities on microorganisms. By analysing DNA sequence similarity features of transposable elements we have identified dramatic genomic changes in bacteria associated with human populations, agriculture and farming, three activities unequivocally linked to the Neolithic Revolution. [More]

IWoCS: analyzing ribosomal ITS configuration and taxonomic relationships

D'Auria et al. (2006) Bioinformatics

In the last ten years the use of ITS sequences for bacterial typing purposes has increased. The 16S-23S Intergenic Transcribed Spacers (ITS) are characterized by a high variability that allows performing intraspecific discrimination of very close bacterial strains. The presence of conserved regions like tRNA genes or boxes together with hyper variable regions makes the ITS a very complex sequence difficult to analyze and compare. [More]

Comparison of prokaryotic diversity at two offshore oceanic locations ..

Zaballos et al. (2006) FEMS Microbiology Ecology

The bacterial and archaeal assemblages at two offshore sites located in polar (Greenland Sea) and Mediterranean (Ionian Sea) waters and two depths (50 and 2000 or 3000m respectively) have been studied by PCR amplification and sequencing of the last 450bp of the 16S rRNA gene. A total of 1817 sequences, together with alignable 16S rRNA gene fragments from the Sargasso Sea metagenome database, were analysed to ascertain variations associated to the geographic location and depth. [More]

The silencing of pseudogenes

Mira and Pushker (2005) Molecular Biology and Evolution

Pseudogenes are non-functional DNA sequences that can accumulate in the genomes of some bacterial species, especially those undergoing processes like niche change, host specialization or weak selection strength. They may last for long evolutionary periods, opening the question of how the genome prevents expression of these degenerated or disrupted genes. [More]

Micro-Mar: a database for dynamic representation of marine microbial biodiversity

Pushker et al. (2005) BMC Bioinformatics

The Micro-Mar database has been created to collect DNA diversity information from marine prokaryotes for geographical and ecological analyses. The database currently includes more than 7000 entries corresponding to high resolution taxonomic genes (16S rRNA, ITS and 23S rRNA) and many other genes including CDS of marine prokaryotes together with available geographical and ecological information. [More]

Comparative genomics of gene-family size

Pushker et al. (2004) Genome Biology

The wealth of genomic data in bacteria is helping microbiologists understand the factors involved in gene innovation. Among these, the expansion and reduction of gene families appears to have a fundamental role in this, but the factors influencing gene family size are unclear. The relative content of paralogous genes in bacterial genomes increases with genome size, largely due to the expansion of gene family size in large genomes. Bacteria undergoing genome. [More]

Evolutionary relationships of Fusobacterium

Mira et al. (2004) BMC Evolutionary Biology

The phylogenetic position and evolutionary relationships of Fusobacteria remain uncertain. Especially intriguing is their relatedness to low G+C Gram positive bacteria (Firmicutes) by ribosomal molecular phylogenies, but their possession of a typical gram negative outer membrane. Taking advantage of the recent completion of Fusobacterium nucleatum genome sequence ... [More]

CoPS: Comprehensive Peptide Signature database

Prakash et al. (2004) Bioinformatics

Comprehensive Peptide Signature Database is an extensive database of 3360 signature peptides, varying in length between 8 to 46 amino acids, representing over 300 functional classes. It provides collating information on the mutation effects on these signature peptides from the Protein Mutant Database (PMD) and identifies the peptide signature(s) occurring in a given biochemical pathway. [More]


Peptide Library Based Homology Search Tool for Function Assignment and Annotation (PLHoSTFA) makes a proteome wise comparison of several organisms and reports the invariant/unique peptide sequences. This tool also assigns suitable function to proteins of yet unknown functions. [More]

DNA synthesis scheduler

ABI 3900 DNA Synthesizer makes 48 oligonucleotides in 4 banks in one run. It requires that the amount of nucleotide of each kind (A, T, C and G) be used in approximately equal amounts for each run of the machine. The software schedules the given oligonucleotides in such a way that for each run amount of each nucleotide used is in approximately equal amount and the wastage is the least. [More]