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Computational Tools: Programs and Software
 | Eagle Eye Sunyaev Lab
Analysis of Complex Protein Mixtures Eagle Eye 1.00 Web link (web-based program) |  | MS-BLAST Sunyaev Lab
Mass Spectrometry Driven BLAST: a specialized BLAST based protocol developed for identification of proteins by sequence similarity searches using peptide sequences produced by the interpretation of tandem mass spectra
MS-BLAST Web link (web-based program)
Reference: (PubMed Link) |  | 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 link (web-based program) Link to References |  | SNP2RFLP Sunyaev Lab
Identification of polymorphic mouse SNPs with Restriction Fragment Length Polymorphism: This program extracts region specific SNPs from the NCBI mouse database that are informative between specified mouse strains AND can be assayed by detection of restriction fragment length polymorphisms.
SNP2RFLP Web link (web-based program) |  | SCONE Sunyaev Lab
Software for comparative genomics. Information and Downloads |  | ModuleFinder Bulyk Lab
This program evaluates the likelihood that a given genomic region is a cis regulatory 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
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