Arakawa K, Tamaki S, Kono N, Kido N, Ikegami K, Ogawa R, Tomita M. Genome Projector: zoomable genome map with multiple views. [BMC Bioinformatics 2009 Jan 23;10(1):31]: Describes Genome Projector, a web-based application with a zoomable user interface based on the Google Maps API that includes four searchable views: a circular genome map, a traditional genome map, a biochemical pathways map, and a DNA walk map. Available here.
Bayjanov JR, Wels M, Starrenburg M, van Hylckama Vlieg JE, Siezen RJ, Molenaar D. PanCGH: a genotype-calling algorithm for pangenome CGH data. [Bioinformatics 2009 Feb 1;25(3):309-14]: Describes software for calling genotypes for pangenome arrays, which contain the DNA of several sequenced reference genomes from the same species in order to study comparative genome hybridization. The algorithm PanCGH incorporates orthology information about genes to predict the presence or absence of orthologous genes in a query organism using pangenome CGH arrays.
Chen TY, Ho JW, Liu H, Xie X. An innovative approach for testing bioinformatics programs using metamorphic testing. [BMC Bioinformatics 2009 Jan 19;10(1):24]: Proposes the use of a new software testing technique, metamorphic testing, to test a range of bioinformatics programs. "Instead of requiring a mechanism to verify whether an individual test output is correct, the MT technique verifies whether a pair of test outputs conform to a set of domain specific properties, called metamorphic relations," according to the abstract. This approach "greatly increases the number and variety of test cases that can be applied."
Chen Y, Chen W, Cobb MH, Zhao Y. PTMap — A sequence alignment software for unrestricted, accurate, and full-spectrum identification of post-translational modification sites. [Proc Natl Acad Sci USA. 2009 Jan 20;106(3):761-6]: Discusses PTMap, a sequence-alignment software package for identifying protein post-translational modifications and polymorphisms. The software performs peak selection, adjustment of inaccurate mass shifts, and precise localization of PTM sites, according to the paper's abstract. "To our knowledge, PTMap is the first algorithm that emphasizes unmatched peaks to eliminate false positives," the abstract states.
Dubchak I, Poliakov A, Kislyuk A, Brudno M. Multiple whole genome alignments without a reference organism. [Genome Res 2009 Jan 28. (e-pub ahead of print)]: Describes a novel symmetric alignment algorithm that does not have the drawbacks of current approaches for multiple sequence alignments, which either require a reference genome or one-to-one mapping between the nucleotides of the genomes. The algorithm is implemented as a part of the VISTA Genome Pipeline, which is available here.
Durinck S, Bullard J, Spellman PT, Dudoit S. GenomeGraphs: integrated genomic data visualization with R. [BMC Bioinformatics 2009, 10:2]: Presents GenomeGraphs, an add-on package for the R statistical programming environment for visualizing genomic datasets in an integrated manner. Available here.
Gehlenborg N, Yan W, Lee IY, Yoo H, Nieselt K, Hwang D, Aebersold R, Hood L. Prequips — An extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data. [Bioinformatics 2009 Jan 6. (e-pub ahead of print)]: Presents an integrative software platform called Prequips for comparative proteomics-based systems biology analysis. The software integrates all information generated from mass-spectrometry-based proteomics as well as from basic proteomics data analysis tools, visualizes this information, and links peptide and protein abundances to external tools. Available here.
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Johnson AD, O'Donnell CJ. An open access database of genome-wide association results. [BMC Med Genet 2009 Jan 22;10(1):6]: Presents a database of 56,411 significant SNP-phenotype associations and accompanying information from 118 genome-wide association studies. "Through preliminary analyses and characterization of available GWAS, we demonstrate the potential to gain new insights by querying a database across GWAS," the authors note in the abstract.
Lee D, Seo H, Park C, Park K. WeGAS: A web-based microbial genome annotation system. [Biosci Biotechnol Biochem 2009 Jan 7 (e-pub ahead of print)]: Introduces WeGAS, or the Web-based microbial Genome Annotation System, which carries out gene prediction, homology search, promoter/motif analysis, genome browsing, gene ontology-analysis based on the COGs and GO, and metabolic pathway-analysis with web-based interfaces. "Major public microbial genome databases can be imported, searched, and browsed through the WeGAS modules," according to the paper's abstract. Available here.
Ma'ayan A, Jenkins SL, Webb RL, Berger SI, Purushothaman SP, Abul-Husn NS, Posner JM, Flores T, Iyengar R. SNAVI: Desktop application for analysis and visualization of large-scale signaling networks. [BMC Syst Biol 2009 Jan 20;3(1):10]: Discusses SNAVI (Signaling Networks Analysis and Visualization), a Windows-based desktop application that uses standard network analysis methods to compute the clustering, connectivity distribution, and detection of biological network motifs. SNAVI can generate linked web pages from network datasets loaded in text format and can create networks from lists of gene or protein names. Available here.
Warren AS, Setubal JC. The Genome Reverse Compiler: an explorative annotation tool. [BMC Bioinformatics 2009 Jan 27;10(1):35]: Describes the Genome Reverse Compiler, an automated genome annotation tool. "Traditionally, to perform whole-genome annotation a user would either set up a pipeline or take advantage of an online service," the abstract states. "With GRC the user need only provide the genome he or she wants to annotate and the function resource files to use." Available here.
Xie X, Rigor P, Baldi P. MotifMap: a human genome-wide map of candidate regulatory motif sites. [Bioinformatics 2009 25(2):167-174]: Describes MotifMap, "the first fairly comprehensive map of regulatory elements in the human genome," according to the paper's abstract. The authors developed a new scoring scheme, the Bayesian branch length score, or BBLS, to predict 1.5 million regulatory sites, corresponding to 380 known regulatory motifs, with an estimated false discovery rate less than 50 percent. "We demonstrate that the method is particularly effective for 155 motifs, for which 121,056 sites can be mapped" with an estimated FDR of less than 10 percent, the abstract states. Available here.
Yeung JM, Sham PC, Chan AS, Cherny SS. OpenADAM: an open source genome-wide association data management system for Affymetrix SNP arrays. [BMC Genomics 2008 Dec 31;9(1):636]: Describes an open source web-based data management system for genotype data generated from the Affymetrix GeneChip Mapping Array and Affymetrix Genome-Wide Human SNP Array platforms. The database supports genotype calling using the DM, BRLMM, BRLMM-P, or Birdseed algorithms provided by Affymetrix Power Tools and includes a new method for genotyping error estimation that is implemented using linkage disequilibrium information from the HapMap project. Available here.