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Bioinformatics Tool-Related Papers of Note, May 2007

Aulchenko YS, Ripke S, Isaacs A, van Duijn CM. GenABEL: an R library for genome-wide association analysis. [Bioinformatics 2007 23(10):1294-1296]: Introduces GenABEL, an R library for genome-wide association analysis on desktop computers. The system was designed to store and handle GWA data, control genetic data quality, test the association of SNPs with binary or quantitative traits, and visualize data. Available here

Férey N, Gros PE, Hérisson J, Gherbi R. Visual Data Mining of Genomic Databases by Immersive Graph-Based Exploration. [ArXiv pre-print archive]: Describes a software package, Genome3DExplorer, that combines data mining and virtual reality visualization. The software “is based on a well-adapted graphical and interaction paradigm, where local and global topological characteristics of data are easily visible, on the contrary to traditional genomic database browsers, always focused on the zoom and details level,” the authors note in the paper’s abstract.

Hu Z, Southerland W. WinDock: Structure-based drug discovery on windows-based PCs. [J Comput Chem. 2007 May 2; (e-pub ahead of print)]: Describes WinDock, a software application designed to help researchers perform high-throughput docking experiments on Windows-based PCs. WinDock combines existing small-molecule searchable 3D libraries, homology modeling tools, and ligand-protein docking programs in a “semi-automatic, interactive manner,” according to the authors.

Khaladkar M, Bellofatto V, Wang JT, Tian B, Shapiro BA. RADAR: a web server for RNA data analysis and research. [Nucleic Acids Res. 2007 May 21 (e-pub ahead of print)]: Describes RADAR, a web server for RNA data analysis and research. The server performs pairwise structure alignment, multiple structure alignment, and database searching and clustering. Available here.

Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. [Nucleic Acids Research 2007 35(9):3100-3108]: Describes RNAmmer, a program for predicting genes for ribosomal RNA. The program uses hidden Markov models trained on data from the 5S ribosomal RNA database and the European ribosomal RNA database project. “Results from running RNAmmer on a large set of genomes indicate that the location of rRNAs can be predicted with a very high level of accuracy,” the authors note in the paper’s abstract. Available here.

Phillippy AM, Mason JA, Ayanbule K, Sommer DD, Taviani E, et al. Comprehensive DNA Signature Discovery and Validation. [PLoS Comput Biol 3(5): e98]: Introduces Insignia, a software system that rapidly identifies DNA signatures in the genomes of bacteria and viruses “that properly differentiate between the target genomes and the sample background.” Available here.

Shah JK, Garner HR, White MA, Shames DS, Minna JD. sIR: siRNA Information Resource, a web-based tool for siRNA sequence design and analysis and an open access siRNA database. [BMC Bioinformatics 2007, 8:178]: Describes the siRNA Information Resource, an open-source database that contains validation information about published siRNA sequences along with a user interface that enables researchers to design and analyze siRNA sequences against a chosen target sequence. The siRNA design tool uses “empirically determined rules derived from a meta-analysis of the published data for existing siRNA probes,” and a weighted scoring system that determines the optimal sequence within a target mRNA, the authors write in the abstract. Available here.


Viswanathan GA, Nudelman G, Patil S, Sealfon SC. BioPP: A Tool for Web-publication of Biological Networks. [BMC Bioinformatics 2007, 8:168]: Presents a software tool for web publication of user-developed large-scale annotated pathway diagrams. The software, Biological Pathway Publisher, converts pathways formatted in the CellDesigner Systems Biology Markup Language into a web-viewable format. “Users have the option to convert their CD-SBML files to HTML for restricted use or to allow their knowledgebase to be web-accessible to the scientific community,” the authors note in the paper’s abstract. Available here.

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