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BioInform s Surfing Report: Web-based Tools from RECOMB 2005


AMOD (Assisted Morpholino Design), from the University of Minnesota, uses translation initiation site predictions and sequence-to-sequence comparisons to aid in putative morpholino identification:

InsPecT, a tag-based tool for analyzing mass spectra, from the University of California, San Diego:

Massome, a database of 162,000 human protein interactions from MIT and Harvard:

Medusa, developed at Columbia University, learns motif models of transcription factor binding sites by incorporating promoter sequence and gene expression data:

MultiBind, from Tel Aviv University, identifies binding patterns common to a set of protein structures:

Notung 2.0, developed at Carnegie Mellon University, is a framework for gene tree reconstruction as well as a phylogenetic analysis tool:

PFAAT, from Pfizer, is an application for analyzing and annotating large protein families:

PSAlign, from Texas A&M University, performs multiple sequence alignment in polynomial time:

SCARNA (Stem Candidate Aligner for RNA), from the University of Tokyo, determines the similarities of the sequences and potential secondary structures for two RNA sequences:

SplitsTree 4.0, from the University of T bingen, is a general framework for tree- and network-oriented phylogenetic analysis:

TOPOFIT-DB is a database of more than 3 million pre-calculated protein structure alignments from Northeastern University:

Filed under

The Scan

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.

TB Resistance Insights Gleaned From Genome Sequence, Antimicrobial Response Assays

Researchers in PLOS Biology explore M. tuberculosis resistance with a combination of sequencing and assays looking at the minimum inhibitory concentrations of 13 drugs.

Mendelian Disease Genes Prioritized Using Tissue-Specific Expression Clues

Mendelian gene candidates could be flagged for further functional analyses based on tissue-specific transcriptome and proteome profiles, a new Journal of Human Genetics paper says.

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.