TFmodeller: comparative modelling of protein–DNA complexes
Interactions between proteins and DNA molecules lie at the core of the fundamental cellular processes such as transcriptional regulation. Some of these interactions have been experimentally described at atomic scale, but the molecular details of many others remain to be discovered. TFmodeller exploits the current knowledge about protein–DNA interfaces contained in the Protein Data Bank and uses it to model similar interfaces related by homology. Results are emailed to the user and include an evolutionary contact matrix, a schematic representation of the putative binding interface and atomic coordinates of the modelled complex. The library of complexes used by TFmodeller is updated on a weekly basis and is available for download. TFmodeller and its web service interface are free for academic users at http://www.ccg.unam.mx/tfmodeller
Bioinformatics 2007 23(13):1694-1696; doi:10.1093/ bioinformatics/btm148
GAzer: gene set analyzer
The basic idea of gene set analysis is to compare two groups by looking at changes in sets of genes, rather than looking at the individual gene level. This type of analysis compensates for the fact that small changes not seen at the gene level are often detected when the gene set as a whole is examined. Another important aspect of gene set analysis is the use of the entire gene set rather than a few hundred selected genes from statistical analysis. Gene set Analyzer (GAzer) is a web-based integrated gene set analysis tool covering all the previously reported parametric and non-parametric models. GAzer can be accessed online at http://integromics.kobic.re.kr/GAzer/
Bioinformatics 2007 23(13):1697-1699; doi:10.1093/ bioinformatics/btm144
msBayes: Pipeline for testing comparative phylogeographic histories
Although testing for simultaneous divergence (vicariance) across different population-pairs that span the same barrier to gene flow is of central importance to evolutionary biology, researchers often equate the gene tree and population/species tree thereby ignoring stochastic coalescent variance in their conclusions of temporal incongruence. In contrast to other available phylogeographic software packages, msBayes is the only one that analyses data from multiple species/population pairs under a hierarchical model.
BMC Bioinformatics 2007, 8:268 doi:10.1186/1471-2105-8-268
BPhyOG: An interactive server for genome-wide inference of bacterial phylogenies based on overlapping genes
BPhyOG is a useful interactive web server for genome-wide inference of any potential evolutionary relationship among the genomes selected by users. It currently includes 177 completely sequenced bacterial genomes containing 79,855 OG pairs, the annotation and homologous OG pairs of which are integrated comprehensively. The reliability of phylogenies complemented by annotations make BPhyOG a powerful web server for genomic and genetic studies. It is freely available at http://cmb.bnu.edu.cn/BPhyOG.
BMC Bioinformatics 2007, 8:266 doi:10.1186/1471-2105-8-266
EasyGO: Gene Ontology-based annotation and functional enrichment analysis tool for agronomical species
EasyGO makes a special contribution to the agronomical research community by supporting Affymetrix GeneChips of both crops and farm animals and by providing stronger capabilities for results visualization and user interaction. Currently it supports 11 agronomical plants, 3 farm animals, and the model plant Arabidopsis. The authors demonstrated EasyGO's ability to uncover hidden knowledge by analyzing a group of probe sets with similar expression profiles. EasyGO is a good tool for helping biologists and agricultural scientists to discover enriched biological knowledge that can provide solutions or suggestions for original problems. It is freely available to all users at http://bioinformatics.cau.edu.cn/easygo/.
BMC Genomics 2007, 8:246 doi:10.1186/1471-2164-8-246
Arabidopsis Gene Family Profiler (aGFP)
In parallel with the rapid accumulation of transcriptomic data, on-line analysis tools are being introduced to simplify their use. Global statistical data analysis methods contribute to the development of overall concepts about gene expression patterns and to query and compose working hypotheses. More recently, these applications are being supplemented with more specialized products offering visualization and specific data mining tools. We present a curated gene family-oriented gene expression database, Arabidopsis Gene Family Profiler (aGFP; http://agfp.ueb.cas.cz), which gives the user access to a large collection of normalised Affymetrix ATH1 microarray datasets. The database currently contains NASC Array and AtGenExpress transcriptomic datasets for various tissues at different developmental stages of wild type plants gathered from nearly 350 gene chips.
BMC Plant Biology 2007, 7:39 doi:10.1186/1471-2229-7-39
Nearest Neighbor Networks: clustering expression data based on gene neighborhoods
An important initial step in the analysis of microarray data is clustering of genes with similar behavior. A number of classical techniques are commonly used to perform this task, particularly hierarchical and K-means clustering, and many novel approaches have been suggested recently. While these approaches are useful, they are not without drawbacks; these methods can find clusters in purely random data, and even clusters enriched for biological functions can be skewed towards a small number of processes (e.g. ribosomes). The Nearest Neighbor Networks algorithm is a valuable clustering method that effectively groups genes that are likely to be functionally related. It is particularly attractive due to its simplicity, its success in the analysis of large datasets, and its ability to span a wide range of biological functions with high precision.
BMC Bioinformatics 2007, 8:250 doi:10.1186/1471-2105-8-250
