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

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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: http://www.secretomes.umn.edu/AMOD/


InsPecT, a tag-based tool for analyzing mass spectra, from the University of California, San Diego: http://peptide.ucsd.edu/inspect.py


Massome, a database of 162,000 human protein interactions from MIT and Harvard: http://www.chip.org/proteomics/massome.html


Medusa, developed at Columbia University, learns motif models of transcription factor binding sites by incorporating promoter sequence and gene expression data: http://www1.cs.columbia.edu/compbio/medusa/


MultiBind, from Tel Aviv University, identifies binding patterns common to a set of protein structures: http://bioinfo3d.cs.tau.ac.il/MultiBind/


Notung 2.0, developed at Carnegie Mellon University, is a framework for gene tree reconstruction as well as a phylogenetic analysis tool: http://goby.compbio.cs.cmu.edu/notung/


PFAAT, from Pfizer, is an application for analyzing and annotating large protein families: http://pfaat.sourceforge.net


PSAlign, from Texas A&M University, performs multiple sequence alignment in polynomial time: http://faculty.cs.tamu.edu/shsze/psalign/


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: http://www.scarna.org/


SplitsTree 4.0, from the University of T bingen, is a general framework for tree- and network-oriented phylogenetic analysis: http://www-ab.informatik.uni-tuebingen.de/software/jsplits/welcome.html


TOPOFIT-DB is a database of more than 3 million pre-calculated protein structure alignments from Northeastern University: http://mozart.bio.neu.edu/topofit/topofit.html

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