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Bioinformatics Tool-Related Papers of Note, February 2008

Cai JJ. PGEToolbox: A Matlab Toolbox for Population Genetics and Evolution. [J Hered. 2008 Feb 29 (e-pub ahead of print)]: Describes PGEToolbox, a Matlab-based open-source software package for data analysis in population genetics. Available here.

Fourment M, Gillings MR. A comparison of common programming languages used in bioinformatics. [BMC Bioinformatics 2008, 9:82]: Describes the comparison of memory usage and speed of execution for three standard bioinformatics methods — the Sellers algorithm, the Neighbor-Joining tree construction algorithm, and an algorithm for parsing Blast file outputs — implemented in six different programming languages: C, C++, C#, Java, Perl, and Python. According to the abstract, implementations in C and C++ were fastest and used the least memory, but programs in these languages contained more lines of code. “Java and C# appeared to be a compromise between the flexibility of Perl and Python and the fast performance of C and C++,” the abstract states.

Ge D, Zhang K, Need AC, Martin O, Fellay J, Urban TJ, Telenti A, Goldstein DB. WGAViewer: A Software for Genomic Annotation of Whole Genome Association Studies. [Genome Res. 2008 Mar 3 (e-pub ahead of print)]: Introduces WGAViewer, a Java-based interface to help researchers annotate, visualize, and interpret the set of P values emerging from a whole-genome association study. According to the paper’s abstract, WGAViewer is able to highlight possible functional mechanisms in an automatic manner and can help in generating hypotheses concerning the possible biological basis of observed associations.

Hamilton NA, Teasdale RD. Visualizing and clustering high throughput sub-cellular localization imaging. [BMC Bioinformatics 2008, 9:81]: Describes a new method, called iCluster, for visualizing, clustering, and comparing large sub-cellular localization image sets. For each member of an image set, iCluster “generates statistics that have been found to be useful in distinguishing sub-cellular localization,” the paper abstract states. The statistics are mapped into two or three dimensions and the complete image set is then visualized using these coordinates. “The result is images that are statistically similar are spatially close in the visualization allowing for easy comparison of images that are similar and distinguishment of dissimilar images into distinct clusters.”

Kalaev M, Smoot M, Ideker T, Sharan R. NetworkBLAST: comparative analysis of protein networks. [Bioinformatics 2008 24(4):594-596]: Discusses the NetworkBLAST web server, which identifies protein complexes in protein-protein interaction networks. The software can analyze a single network or two networks from different species, according to the authors. Available here.

Lai W, Choudhary V, Park PJ. CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms. [Bioinformatics. 2008 Feb 22 (e-pub ahead of print)]: Describes CGHweb, a web-based visualization tool that applies several algorithms to a single array-CGH profile entered by the user and generates a heatmap panel of the segmented profiles for each method as well as a consensus profile. Available here

Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. [Bioinformatics 2008 24(5):713-714)]: Describes SOAP, a program for gapped and ungapped alignment of short oligonucleotides onto reference sequences. The program is designed to handle short reads generated by the Illumina Genome Analyzer and is compatible with numerous applications, including single-read or pair-end resequencing, small RNA discovery, and mRNA tag sequence mapping. Available here   

Liu Q, Olman V, Liu H, Ye X, Qiu S, Xu Y. RNACluster: An integrated tool for RNA secondary structure comparison and clustering. [J Comput Chem. 2008 Feb 13 (e-pub ahead of print]: Describes RNACluster, a platform that compares different distances between RNA secondary structures and performs cluster identification to gain useful information of RNA structure ensembles. The software “provides a user-friendly graphical interface to allow a user to compare different structural distances, analyze the structure ensembles, and visualize predicted structural clusters,” according to the abstract.

Morris JS, Clark BN, Gutstein HB. Pinnacle: a fast, automatic and accurate method for detecting and quantifying protein spots in 2-dimensional gel electrophoresis data. [Bioinformatics 2008 24(4):529-536]: Describes a new method for spot detection and quantification in 2D gel analysis called Pinnacle. The spot definition “is based on simple, straightforward criteria rather than complex arbitrary definitions, and results in no missing data,” according to the authors.

Rohde C, Zhang Y, Jurkowski TP, Stamerjohanns H, Reinhardt R, Jeltsch A. Bisulfite sequencing Data Presentation and Compilation (BDPC) web server--a useful tool for DNA methylation analysis. [Nucleic Acids Res. 2008 Feb 22 (e-pub ahead of print)]: Describes the Bisulfite sequencing Data Presentation and Compilation, or BDPC, web interface, which automatically analyzes bisulfite datasets prepared using the BiQ Analyzer. Available here


Zhang S, Kumar K, Jiang X, Wallqvist A, Reifman J. DOVIS: an implementation for high-throughput virtual screening using AutoDock. [BMC Bioinformatics 2008, 9:126]: Discusses an application called DOcking-based VIrtual Screening, or DOVIS, that uses the AutoDock docking engine and runs in parallel on a Linux cluster. According to the abstract, DOVIS can efficiently dock millions of small molecules to a receptor, screening 500 to 1,000 compounds per processor per day.

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