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Bioinformatics Tool-Related Papers of Note, December 2006

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Baran R, Kochi H, Saito N, Suematsu M, Soga T, Nishioka T, Robert M, Tomita M. MathDAMP: a package for differential analysis of metabolite profiles. [BMC Bioinformatics 2006, 7:530]: Describes a software package called MathDAMP (Mathematica package for Differential Analysis of Metabolite Profiles), which highlights differences between raw mass spec datasets analyzing corresponding signal intensities “on a datapoint-by-datapoint basis” in order to bypass peak identification and integration, the authors note.
 

 
Eronen L, Geerts F, Toivonen H. HaploRec: Efficient and accurate large-scale reconstruction of haplotypes. [BMC Bioinformatics 2006, 7:542]: Describes three statistical models and an algorithm for haplotype reconstruction, jointly called HaploRec. HaploRec uses “local regularities” in order to reconstruct haplotypes so that they have maximal local coherence, the authors note in the paper’s abstract. Availability: http://www.cs.helsinki.fi/group/genetics/haplotyping.html.
 

 
Good BM, Kawas EA, Kuo BY, Wilkinson MD. iHOPerator: User-scripting a personalized bioinformatics Web, starting with the iHOP website. [BMC Bioinformatics 2006, 7:534]: Describes an effort to enhance the content and presentation of the iHOP (information Hyperlinked Over Proteins) website using the GreaseMonkey Firefox extension for developing and deploying user scripts. The iHOPerator user script “augments the gene-centered pages on iHOP by providing a compact, configurable visualization of the defining information for each gene and by enabling additional data, such as biochemical pathway diagrams, to be collected automatically from third party resources and displayed in the same browsing context,” the authors note in the paper’s abstract.
 

 
Hua J, Craig DW, Brun M, Webster J, Zismann V, Tembe W, Joshipura K, Huentelman MJ, Dougherty ER, Stephan DA. SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays. [Bioinformatics 2007 23(1):57-63]: Introduces a SNP genotype-calling program called SNiPer-High Density for calling genotypes across hundreds of thousands of SNPs. The program uses an expectation-maximization algorithm with parameters based on a training sample set. The method also uses a quality-control metric for each assayed SNP, so that “poor-behaving” SNPs can be filtered, the authors note in the abstract. Availability: http://www.tgen.org/neurogenomics/data
 

 
Huttenhower C, Hibbs M, Myers C, Troyanskaya OG. A scalable method for integration and functional analysis of multiple microarray datasets. [Bioinformatics 2006 22(23):2890-2897]: Presents Microarray Experiment Functional Integration Technology, a Bayesian framework for predicting functional relationships from integrated microarray datasets. All results are provided in the context of specific biological functions, which can be provided by a biologist or drawn automatically from resources such as the Gene Ontology. The authors describe the use of MEFIT to integrate 40 Saccharomyces cerevisiae microarray datasets spanning 712 unique conditions. Availability: http://function.princeton.edu/mefit/.
 

 
Jabado OJ, Palacios G, Kapoor V, Hui J, Renwick N, Zhai J, Briese T, Lipkin WI. Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments. [Nucleic Acids Research 2006 34(22):6605-6611]: Describes a software package for designing degenerate primers for large groups of related targets based on complex multiple sequence alignments. The method is based on tree building followed by a set-covering algorithm.
 

 
Jenett A, Schindelin JE, Heisenberg M. The Virtual Insect Brain Protocol: creating and comparing standardized neuroanatomy. [BMC Bioinformatics 2006, 7:544]: Describes the Virtual Insect Brain protocol, a script suite for the quantitative assessment, comparison, and presentation of neuroanatomical data. The suite is based on the 3D-reconstruction and visualization software Amira from Mercury. The protocol has been developed for standardizing Drosophila neuroanatomy, but it can also be used for other 3D structures, the authors note. Availability: http://www.neurofly.de/.
 

 
Letunic I, Bork P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. [Bioinformatics 2007 23(1):127-128]: Describes the Interactive Tree of Life, a web-based tool for displaying, manipulating, and annotating phylogenetic trees. Availability: http://itol.embl.de/
 

 
Sanford C, Yip ML, White C, Parkinson J. Cell++—simulating biochemical pathways. [Bioinformatics 2006 22(23):2918-2925]: Introduces Cell++, a stochastic simulation environment for studying biochemical processes within a spatial context. Availability: http://www.compsysbio.org/CellSim/
 

 
Song CM, Yeo BH, Tantoso E, Yang Y, Lim YP, Li KB, Rajagopal G. iHAP – integrated haplotype analysis pipeline for characterizing the haplotype structure of genes. [BMC Bioinformatics. 2006 Dec 1;7:525]: Describes a system for analyzing HapMap data in order to characterize the haplotype structure of genes or chromosomal regions. The system, called iHAP, includes genotype and haplotype data from the HapMap project and gene information from the UCSC Genome Browser Database, as well as capabilities for inferring haplotype blocks and selecting tag SNPs that are representative of haplotype patterns. Availability: http://ihap.bii.a-star.edu.sg/.
 

 
Wang X, He H, Li L, Chen R, Deng XW, Li S. NMPP: a user-customized NimbleGen microarray data processing pipeline. [Bioinformatics 2006 22(23):2955-2957]: Describes NMPP, a bundle of tools based on established algorithms and methods to process self-designed NimbleGen microarray data. The package includes a command-line-based integrative processing procedure that comprises five functional components: raw microarray data parsing and integrating; array spatial effect smoothing and visualization; probe-level multi-array normalization; gene expression intensity summarization; and gene expression status inference. Availability: http://plantgenomics.biology.yale.edu/nmpp
 

 
Yip KY, Yu H, Kim PM, Schultz M, Gerstein M. The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks. [Bioinformatics 2006 22(23):2968-2970]: Describes TopNet-like Yale Network Analyzer, a web-based system for managing, comparing, and mining multiple cellular networks. The tYNA system can manage a large number of private and public networks using a flexible tagging system, filter them based on a variety of criteria, and visualize them through an interactive graphical interface. Availability: http://networks.gersteinlab.org/tyna.

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