Polyphen
Sunyaev Lab/Bork Group
Polymorphism Phenotyping
This program may be used to predict the impact of an amino acid substitution on the structure and function of a protein using straightforward physical and comparative considerations.
PolyPhen (web-based program)
SNPtrack
Interface for mutation mapping and identifying causal mutations from whole-genome sequencing studies.
SNPtrack (web-based program)
ModuleFinder
Bulyk Lab
This program evaluates the likelihood that a given genomic region is a cisregulatory module for an input set of transcription factors according to its degree of: (1) homotypic site clustering; (2) heterotypic site clustering; and (3) evolutionary conservation across multiple genomes.
Link to ModuleFinder Software Download Page
Reference: Philippakis AA, He FS, Bulyk ML. Modulefinder: a tool for computational discovery of cis regulatory modules. Pac Symp Biocomput. 2005; 519-30.
PubMed Link
MultiFinder
Bulyk Lab
This software performs automated motif searching using four different profile-based motif finders, including AlignACE, MDscan, BioProspector and MEME. We anticipated that using all four of these motif finders might allow the user to combine the strengths of their different algorithms.
Link to MultiFinder Software Download Page
Reference: Huber BR and Bulyk ML. Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data. BMC Bioinformatics 2006 Apr 27; 7: 229.
PubMed Link
