Skip to main content
Premium Trial:

Request an Annual Quote

BioInform s Surfing Report: New Web-Based Tools from RECOMB 2002


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:

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:

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:

• UC Berkeley’s Lior Pachter discussed his SLIM algorithm for designing minimum networks for the search spaces of HMM-based alignment algorithms:

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:



• 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:

Kazuharu Arakawa of Keio University has developed an object-oriented “generic genome analysis environment” called G-language:

• 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:

Anna Barbasiewicz of the University of Montreal has released Gopop, a web-based application used to automate database population for the Gobase organelle database:

• MGR software for constructing phylogenies based on multiple genome rearrangements is available from the University of Southern California’s Guillaume Bourque at:

• 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:

• 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:

David Gilbert of the University of Glasgow has designed a pattern-matching algorithm to compare structures within the TOPS (Topology of Protein Structures) database:

• Genomic Object Net, software from Satoru Miyano at the University of Tokyo, was developed for biopathway modeling and simulation:

Filed under

The Scan

Long COVID-19 Susceptibility Clues Contained in Blood Plasma Proteome

A longitudinal study in eBioMedicine found weeks-long blood plasma proteome shifts after SARS-CoV-2 infection, along with proteomic signatures that appeared to coincide with long Covid risk.

Tibetan Study Finds Adaptive Variant Influencing Skin Pigmentation

With a combination of phenotyping and genetic data, researchers document at PNAS a Tibetan-enriched enhancer variant influencing melanin synthesis and ultraviolet light response.

Domestication Linked to Nervous System Genes in Inbred Mouse Strains

Researchers highlighted more than 300 positively selected genes in domesticated mice, including genes linked to nervous system function or behavior in Genome Biology.

ALS Genetic Testing May Be Informative Across Age Ranges, Study Finds

Researchers in the journal Brain identified clinically actionable variants in a significant subset of older ALS patients, prompting them to point to the potential benefits of broader test use.