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

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Bhaduri A, Pugalenthi G, Sowdhamini R. PASS2: an automated database of protein alignments organised as structural superfamilies. [BMC Bioinformatics 2004, 5:35]: Introduces the PASS2 (Protein Alignment organized as Structural Superfamily) database, which represents continuously updated, structural alignments for evolutionary related, sequentially distant proteins. Availability: http://www.ncbs.res.in/~faculty/mini/campass/pass2.html.


Biro JC, Biro JM. A novel sequence similarity searching and visualization method based on overlappingly translated nucleic acids: the blastNP. [Med Hypotheses 62(4): 568-74]: Describes BlastNP, an alternative to TblastX that translates nucleic acid sequences into overlapping protein-like sequences before searching with BlastP. According to the authors, blastNP is more sensitive than TblastX for detecting short sequence similarities (less than 50 residues).


Bowers P, et al. Prolinks: a database of protein functional linkages derived from coevolution. [Genome Biology 2004, 5:R35]: Discusses an approach for determining protein function that combines four algorithms (phylogenetic profile, Rosetta Stone, gene neighbor, and gene cluster) in a single database called Prolinks that spans 83 organisms and includes 10 million “high-confidence” links. Availability: http://dip.doe-mbi.ucla.edu/pronav.


Dugas M, et al. mdclust — exploratory microarray analysis by multidimensional clustering. [Bioinformatics 20(6): 931-6]: Discusses multidimensional clustering (mdclust), a method that identifies sets of sample clusters and associated genes for analyzing microarray data. Availability: http://martin-dugas.de/mdclust/.


Gromiha MM, Ahmad S, Suwa M. Neural network-based prediction of transmembrane beta-strand segments in outer membrane proteins. [J Comput Chem. 25(5): 762-7]: Proposes a method based on neural networks for predicting membrane-spanning beta-strands in outer membrane proteins based on the concept of “residue probability,” which assigns residues in transmembrane beta-strand segments. Availability: http://psfs.cbrc.jp/tmbeta-net/.


Huang H, et al. Identifying transcriptional regulatory sites in the human genome using an integrated system. [Nucleic Acids Research 2004 32(6): 1948-1956]: Introduces a system for predicting co-occurrence of transcriptional regulatory sites by integrating several known site-matching, over-presented oligonucleotide detection, and DNA motif-discovery programs. Availability: http://rgsminer.csie.ncu.edu.tw/.


Lau A, Chasman D. Functional classification of proteins and protein variants. [PNAS 101(17): 6576-6581]: Introduces a method that defines criteria for functional relatedness among proteins using phylogenetic information, along with a companion procedure for predicting deleterious alleles or mutations.


Panchenko AR, Kondrashov F, Bryant S. Prediction of functional sites by analysis of sequence and structure conservation. [Protein Sci. 13(4): 884-92.]: Presents a method for predicting functional sites in a set of aligned protein sequences based on the selection of sites that are both well conserved and clustered together in space, as inferred from the 3D structures of proteins included in the alignment.


Richard JS, et al. Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data. [Genome Biology 2004, 5:R37]: Describes Genome2D, a Windows-based software tool for visualizing bacterial transcriptome and customized datasets on linear chromosome maps. Availability: http://molgen.biol.rug.nl/molgen/research/molgensoftware.php.


Riva AA, Kohane IS. A SNP-centric database for the investigation of the human genome. [BMC Bioinformatics 5(1): 33]: Introduces SNPper, a web-based database of human SNPs along with querying, visualization, and data-export tools. Availability: http://snpper.chip.org/.


Silva DG, et al. Identification of “pathologs” (disease-related genes) from the RIKEN mouse cDNA dataset using human curation plus FACTS, a new biological information extraction system. [BMC Genomics 2004 5(1): 28]: Describes the use of mouse transcriptome data from Riken’s Fantom2 project to identify novel human disease-related candidate genes. The researchers developed a biological information extraction and annotation tool called FACTS (Functional Association/Annotation of cDNA Clones from Text/Sequence Sources) that was used in parallel with human expert analysis to identify 182 candidate genes. Availability: http://facts.gsc.riken.go.jp/.


Smoot M, Guerlain S, Pearson W. Visualization of near-optimal sequence alignments. [Bioinformatics 20(6): 953-8]: Introduces web-based software that displays near-optimal or alternative alignments of two protein or DNA sequences as a continuous moving picture. A Java applet displays alignments in a series of frames so that consistently aligned regions remain at a fixed position on the display, while variable regions move. Availability: http://fasta.bioch.virginia.edu/noptalign.


Tang C, Zhang A, Ramanathan. ESPD: a pattern detection model underlying gene expression profiles. [Bioinformatics 20(6): 829-38]: Proposes a microarray analysis method called empirical sample pattern detection (ESPD) that integrates statistical metrics, data mining, and machine learning techniques to determine the relationship between samples and genes. Availability: upon request.


Young N, Chang Z, Wishart D. GelScape: a web-based server for interactively annotating, manipulating, comparing and archiving 1D and 2D gel images. [Bioinformatics 20(6): 976-8]: Presents GelScape, a web-based tool for annotating, comparing, manipulating, and storing protein gel images. Availability: http://www.gelscape.ualberta.ca.


Zhou M, Cui Y. GeneInfoViz: Constructing and visualizing gene relation networks. [In Silico Biol. 4(2):0026]: Describes GeneInfoViz, a web tool for batch retrieval of gene information and construction and visualization of gene relation networks. Availability: http://genenet.org/.

 

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