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In Print: Bioinformatics Tool-Related Papers of Note, August 2004


Chou K, Cai Y. Prediction of protein subcellular locations by GO-FunD-PseAA predictor. [Biochem Biophys Res Commun. 2004 320(4):1236-9]: Describes an automated method for predicting the subcellular location of proteins based on a combination of three previously developed methods: a gene ontology approach; a functional domain composition approach; and a pseudo-amino acid composition approach.

Coventry A, et al. MSARI: Multiple sequence alignments for statistical detection of RNA secondary structure. [Proc. Natl. Acad. Sci. USA 2004 101 (33): 12102-12107]: Presents MSARI, a program that identifies genes with conserved RNA secondary structure by searching multiple sequence alignments of a set of candidate orthologs for correlated arrangements of reverse-complementary regions. Availability:

Hansen M, Smedsgaard J. A new matching algorithm for high resolution mass spectra. [J Am Soc Mass Spectrom. 2004 15(8):1173-80]: Discusses a new matching algorithm, the accurate mass spectrum distance method, designed to compare high-resolution spectra independent of any alignment.

Higa R, et al. Sting Millennium Suite: integrated software for extensive analyses of 3D structures of proteins and their complexes. [BMC Bioinformatics. 2004 5(1):107]: Describes the Sting Millennium Suite, web-based software for molecular structure and sequence/structure/function analysis.

Lehner B, Fraser A. A first-draft human protein-interaction map. [Genome Biology 2004, 5:R63]: Introduces a network of more than 70,000 predicted physical interactions between around 6,200 human proteins generated using the data from lower eukaryotic protein-interaction maps. Availability:

Leipzig J, Pevzner P, Hever S. The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome. [Nucleic Acids Research 2004 32(13):3977-3983]: Describes a database of splicing graphs for human genes, using transcript information from various major sources (Ensembl, RefSeq, STACK, TIGR and UniGene). Availability:

Li LM, Kim JH, Waterman MS. Haplotype reconstruction from SNP alignment. [J Comput Biol. 2004;11(2-3):505-16]: Describes a method for statistical reconstruction of haplotypes from a set of aligned SNP fragments based on a statistical model of sequencing errors, compositional information, and haplotype memberships.

Liebel U, Kindler B, Pepperkok R. ‘Harvester’: a fast meta search engine of human protein resources. [Bioinformatics. 2004 20(12):1962-3]: Presents Harvester, a web-based tool that collects bioinformatics data on human proteins from various databases and prediction servers. Availability:

Middendorf M, Ziv E, Wiggins C. Inferring Network Mechanisms: The Drosophila melanogaster Protein Interaction Network. [arXiv pre-print archive:]: Describes a method for inferring the mechanism most accurately capturing a given network topology, exploiting discriminative tools from machine learning.

Reeder J, Giegerich R. Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. [BMC Bioinformatics 2004, 5:104]: Introduces an algorithm to predict the energetically optimal structure of an RNA sequence containing pseudoknots “of medium size.”

Stevens R, et al. Exploring Williams-Beuren syndrome using myGrid. [Bioinformatics. 2004 20 Suppl 1:I303-I310]: A demonstration of the use of the myGrid middleware in the context of a series of bioinformatics experiments focused on a 1.5 Mb region on chromosome 7 that is deleted in Williams-Beuren syndrome. Availability:

Zhou Q, Wong W. CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling. [Proc. Natl. Acad. Sci. USA 2004 101 (33):12114-12119]: Discusses a new de novo motif-module discovery algorithm, CisModule, which uses a hierarchical mixture approach to model the cis-regulatory module structure. Availability:


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