Last week, 650 computational scientists gathered in San Diego for the eighth annual Conference on Research in Computational Molecular Biology — an attendance record, according to organizers. The meeting attracts the world’s leading bioinformatics algorithmists, and is a hotbed for emerging methods that may turn out to be tomorrow’s bioinformatics workhorses. A sampling of some web-based tools discussed at the conference follows.
BOMP (Beta-Barrel Outer Membrane Protein Predictor), from the University of Bergen, predicts whether a sequence from a Gram-negative bacterium is a beta-barrel outer membrane protein: http://www.bioinfo.no/tools/bomp.
Genome Fingerprint Scanning, a gene-finding method that uses peptide mass fingerprint data to identify genes in partially sequenced genomes, from the University of North Carolina at Chapel Hill: http://gfs.unc.edu.
CAMP (Comparative Analysis of Metabolic Pathways) calculates the similarities and differences between multiple metabolic pathways in KEGG, from National Yang-Ming University in Taiwan: http://gel.ym.edu.tw/camp.
Clann, from the National University of Ireland in Maynooth, identifies horizontal gene transfer events via supertree analysis: http://bioinf.may.ie/software/clann.
e2g, a tool for aligning genomic sequence with cDNA and EST databases, from Bielefeld University: http://bibiserv.techfak.uni-bielefeld.de/e2g/.
NCBI has developed a system for identifying gene or protein names that are closely related to a query gene name: http://web.ncbi.nlm.nih.gov/IRET/Gene_Prot_Match/.
GOArray, from Yale University, identifies genes associated with a term in the Gene Ontology database: http://ycmi.med.yale.edu/gomine/.
PhlyoBlocks, from Argonne National Laboratory, analyzes protein function using phylogenetic information: http://compbio.mcs.anl.gov/ulrich/phyloblock.
SVMmer, from Argonne National Laboratory, classifies protein families using a support vector machine algorithm: http://compbio.mcs.anl.gov/svmmer.
GOAT (Genome Organization Analysis Tool) compares one or more query genomes against a reference genome to produce a two-dimensional dot plot of matches relative to the reference genome, from Virginia Tech: http://gaia.biotech.vt.edu/goat/.
TsukubaBB, from AIST in Japan, is a simple heuristic algorithm for motif extraction: http://seq.cbrc.jp.
Prober extracts degenerate probes among a set of multiple sequences, from the University of Ulsan College of Medicine in Korea: http://prober.biocodes.org.
GLP (Generalized Local Propensity), from the University of Kansas, identifies sequence segments with high and low conformational flexibility: http://jay.bioinformatics.ku.edu/~gerlach/propensity.html.
HMMerHEAD (HMMer Hashing Enabled Acceleration Device), filters out sequences for HMMer’s hmmsearch program to speed running time 15-fold, from Hebrew University: http://www.cs.huji.ac.il/labs/compbio/hmmerhead.
ELXR (Exon Locator and Extractor for Resequencing) automates primer set selection, from the University of Texas Southwestern Medical Center: http://elxr.swmed.edu/.
OPAAS (Optimal, Permuted, and Alternative Alignment of protein Structure), from the Institute of Biomedical Sciences in Taiwan, is a protein structure comparison method based on probability-based matching of secondary structure elements: http://gln.ibms.sinica.edu.tw/software.php.
PairFold, an algorithm for secondary structure prediction of pairs of RNA molecules, from the University of British Columbia: http://www.RNAsoft.ca.
The Protein Mutant Resource (PMR), from the San Diego Supercomputer Center, characterizes related artificially mutated structures from the PDB by grouping point mutations of the same structure: http://pmr.sdsc.edu.
EcoTFs (Escherichia coli Transcription Factors and Signals), from Los Alamos National Laboratory, contains data on 50 transcription factors in E. coli: http://EcoTFs.lanl.gov.
MPromDb is a database of mammalian promoters with annotation of the first exon and experimentally supported cis-regulatory elements, from Ohio State University: http://bioinformatics.med.ohio-state.edu/databases/index.html.