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Practically Genomic … A hands-on Bioinformatics IAP

Practically Genomic … A hands-on Bioinformatics IAP. Course Materials: http://luria.mit.edu/Jan_07_IAP Instructors: Charlie Whittaker and Sebastian Hoersch MIT Center for Cancer Research Bioinformatics and Computing Core Facilty E18-366 Students - Wide range of experience levels

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Practically Genomic … A hands-on Bioinformatics IAP

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  1. Practically Genomic…A hands-on Bioinformatics IAP • Course Materials: http://luria.mit.edu/Jan_07_IAP • Instructors: Charlie Whittaker and Sebastian Hoersch MIT Center for Cancer Research Bioinformatics and Computing Core Facilty E18-366 • Students - Wide range of experience levels • Evaluations - Please send comments to charliew@mit.edu

  2. Agenda During this course, we will: • Use Excel to manipulate lists of genes and map different kinds of identifiers to one another. • Retrieve protein sequences from the Uniprot database. • Access protein annotations using the Proteome database. • Use Gene Ontology Tree Machine to characterize functions attributed to genes in a list. • Use the UCSC Genome Browserto visualize and query genomic data. • Annotate genomic sequence using ARGO. • Perform sequence alignments and phyolgenetic analyses (BLAST, ClustalW, NJplot). • Analyze protein domains and motifs using SMART, Interpro and Scansite.

  3. Prabhakar et al., 2006 • The starting material for these activities is data from a November ‘06 Science paper. • This paper characterizes conserved non-coding sequences that are undergoing accelerated evolution in the human lineage. • The first part of this work was to identify conserved non-coding sequences. 110,549 such sequences were identified.

  4. Conserved Non-coding Sequences

  5. Accelerated Evolution in Humans ZOOM in ~10x Table S1A ranks 992 CNSs and lists their nearest Refseq Gene

  6. Functional Classification of Proteins • Database records • Literature • GO (http://www.geneontology.org/)“The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism. [...] The GO project has developed three structured, controlled vocabularies (ontologies) that describe gene products in terms of their associated biological processes, cellular components and molecular functions in a species-independent manner.” • Prabhakar note that neuronal cell adhesion proteins are overrepresented in the list of genes near the 992 CNSs undergoing accelerated evolution in the human lineage. Available information and nomenclature used dependent on researcher, research focus, species etc.

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