Software

Eagle Eye

Sunyaev Laboratory
Analysis of Complex Protein Mixtures

Eagle Eye 1.0 (Web-based program)

MS-BLAST

Sunyaev Lab

Mass Spectrometry Driven BLAST: a specialized BLAST based protocol developed for identification of proteins by sequence similarity searchers using peptide sequences prodcued by the interpretation of tandem mass spectra

MS-BLAST (Web-based program)

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)

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-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 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