Attendees of RECOMB 2002 were presented with a number of new tools to try out via the websites of their developers. A sampling of some cutting-edge technology from the conference follows.
• Purdue University’s Alberto Apostolico and his colleagues have put together a suite of tools to detect “unusual” (unexpectedly rare or common) words in genetic sequences: www.cs.ucr.edu/~stelo/Verbumculus.
• Peter Arndt of UC San Diego discussed a method that uses neighbor-dependent mutation processes to calculate dinucleotide frequencies. The tool, which can also use the dinucleotide frequencies to model neighbor-dependent mutation, is available at: http://bioinfo.ucsd.edu/dinucleotides.
• Jeremy Buhler of Washington University has released an implementation of his LSH-ALL-PAIRS-SIM algorithm that applies a scoring function to sensitively find local similarities in large biosequence collections: www.cs.wustl.edu/~jbuhler/projection.html.
• UC Berkeley’s Lior Pachter discussed his SLIM algorithm for designing minimum networks for the search spaces of HMM-based alignment algorithms: http://bio.math.berkeley.edu/slim.
• Alexander Zien and his colleagues at Fraunhofer-Gesellschaft have developed a Java applet for researchers to determine the optimal sample size of microarray experiments for a given set of parameters: http://cartan.gmd.de/~zien/classsize/calculator.html.
• MAM (Multiple Alignment Manipulator), a tool for constructing and analyzing multiple sequence alignments of genomic DNA, is available from Can Alkan and colleagues at Case Western Reserve University at: http://genomics.cwru.edu/MAM.html.
• Kazuharu Arakawa of Keio University has developed an object-oriented “generic genome analysis environment” called G-language: www.g-language.org.
• LORIA’s (Laboratoire Lorrain de Recherche en Informatique et Ses Applications) Gregory Kucherov has released MREPS, a program for characterizing tandem repeats in a given DNA sequence at: www.loria.fr/~kucherov/software/mreps.
• Anna Barbasiewicz of the University of Montreal has released Gopop, a web-based application used to automate database population for the Gobase organelle database: http://megasun.bch.umontreal.ca/gobase.
• MGR software for constructing phylogenies based on multiple genome rearrangements is available from the University of Southern California’s Guillaume Bourque at: www-cse.ucsd.edu/groups/bioinformatics/MGR.
• USC’s Glenn Tesler’s GRIMM (Genome Rearrangements in Man and Mouse) web server, which determines the minimal rearrangement distance for numerous combinations of genome types, is at:
• Stanford’s Michael Brudno has released CHAOS (CHAins Of Scores), an heuristic algorithm for local alignment for intronic and intergenic DNA: www.stanford.edu/~brudno/chaos.
• Superlink, a program that performs linkage analysis on larger files than possible with standard genetic linkage programs such Linkage, Fastlink, and Vitesse, is available from Ma’ayan Fischelson at Technion: www.cs.technion.ac.il/~fmaayan/Superlink.html.
• David Gilbert of the University of Glasgow has designed a pattern-matching algorithm to compare structures within the TOPS (Topology of Protein Structures) database: www.tops.leeds.ac.uk.
• Genomic Object Net, software from Satoru Miyano at the University of Tokyo, was developed for biopathway modeling and simulation: www.genomicobject.net.