lit_disc_quiz_2

lit_disc_quiz_2 - How did they identify putative regulatory...

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7.91/BE.490: Foundations of Computational and Systems Biology Literature Discussion Quiz 03/16/2004 To be turned in at the beginning of class Paper #1 Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature. 2003 May 15;423(6937):241-54. Sequencing and comparison of yeast species to identify genes and regulatory elements. Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. This paper describes the sequencing of how many new genomes? How were the species chosen (in terms of sequence similarity) and why? Briefly describe how the authors determine the evolutionary relationship and distance between the species analyzed. What was their approach to determine whether an ORF encoded a protein or was found by chance?
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Unformatted text preview: How did they identify putative regulatory motifs? Explain briefly. Paper #2 Computational identification of noncoding RNAs in E. coli by comparative genomics. Curr Biol. 2001 Sep 4;11(17):1369-73. Computational identification of noncoding RNAs in E. coli by comparative genomics. Rivas E, Klein RJ, Jones TA, Eddy SR. The authors perform a computational comparative genomic screen for ncRNA genes. What kind of mutations that usually occur in ncRNAs do they take advantage of? Why do these kinds of mutations often appear in ncRNA genes? Briefly describe the approach they use to identify ncRNAs in E. coli. How do the authors test their predictions? What are the problems with this approach?...
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This note was uploaded on 11/11/2011 for the course BIO 2.797j taught by Professor Matthewlang during the Fall '06 term at MIT.

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