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Sunyaev Lab

Location: NRB 0466B, 77 Ave Louis Pasteur, Boston, MA 02115

Summary:

We are interested in structural and evolutionary analysis of genome variation and divergence. We apply bioinformatic approaches to problems of evolutionary genetics and human population genetics.
Additionally we develop novel computational techniques for proteomics and for comparative analysis of protein sequences and structures.

Affiliations:

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Protocols

Software

  • EagleEye ( Algorithmic software component )

    "Apart from useful MS/MS spectra, LC-MS/MS runs produces loads of spectra whose identity either remains unknown, or that could be traced to some typical background proteins, like trypsin, keratins and other proteins from human skin, sheep keratins from wool clothes etc. Background spectra slow down database searches, elevate false discovery rate and, in sequence similarity searches, produce weird “orphan” hits of unclear origin. EagleEye removes background MS/MS spectra by comparing them with a non-annotated collection of spectra, obtained from combined LC-MS/MS runs of control in-gel digests as well as identified in on-going proteomis projects."

  • MS-BLAST ( Algorithmic software component )

    "MS-BLAST: Mass Spectrometry driven BLAST: a specialised BLAST –based protocol developed for identification of proteins by sequence similarity searches using peptide sequences produced by the interpretation of tandem mass spectra."

  • PolyPhen-2 ( Algorithmic software component )

    "PolyPhen-2 (Polymorphism Phenotyping v2) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations. Please, use the form below to submit your query."

  • SCONE ( Algorithmic software component )

    "SCONE (Sequence CONservation Evaluation) estimates the rate at which each nucleotide position is evolving. It computes the probability of neutrality given this rate estimate, and summarizes the result in a Sequence CONservation Evaluation (SCONE) score"

  • SNP2RFLP ( Algorithmic software component )

    "Single nucleotide polymorphism (SNP) markers give high resolution in genetic mapping in mouse because they are abundant and easily typed. Initial localization via a genome-wide SNP panel often defines a large chromosomal interval and insufficient informative markers with which to proceed with fine-mapping. To further refine this interval containing a mutation that is causative for a phenotype of interest, SNP2RFLP extracts region-specific SNPs from the NCBI mouse SNP database that are informative between the mouse strains used in the cross. SNP2RFLP then identifies those SNPs that create restriction fragment length polymorphisms (RFLPs) that can be easily assayed at the benchtop via restriction enzyme digestion of SNP-containing PCR products. "


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Last updated: 2012-10-18T14:19:55.940-05:00

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The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016