CO331 - Bioinformatics, Jan-May, 2015

Welcome to the CO331 - Bioinformatics, Jan-May, 2015 course page.

Course Syllabus

Introduction to Bioinformatics. Introduction to Algorithms and Complexity. Restriction mapping and motif finding algorithms. Greedy Algorithms in Genome Assembly. DNA Sequence comparison: Dynamic programming approaches. Sequence Alignment - Graph algorithms. Combinatorial pattern matching. Clustering and trees in Gene expression analysis. Randomized algorithms in Bioinformatics. Hidden Markov Models.

Reference Material

Reference Books/Textbooks:

  • Neil C. Jones and Pavel A. Pevzner. An Introduction to Bioinformatics Algorithms. MIT Press, 2004. ISBN-10: 0262101068, ISBN-13: 978-0262101066.
  • David W Mount. Bioinformatics: Sequence and Genome Analysis. Cold Spring Harbor Laboratory Press,U. S. 2nd Revised edition. 2004. ISBN-10: 0879697121. ISBN-13: 978-0879697129.
  • Marketa Zvelebil and Jeremy Baum. Understanding Bioinformatics. Garland Science, 1st Edition, 2007. ISBN-10: 0-8153-4024-9, ISBN-13: 978-0-8153-4024-9.
  • Mitchell L Model. Bioinformatics Programming Using Python. O'Reilly.

Other References:

  • Phillip Compeau and Pavel Pevzner, Bioinformatics Algorithms
  • David Sankoff, and Joseph Kruskal. Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison. The Center for the Study of Language and Information Publications; New edition. 2000. ISBN-10: 1575862174. ISBN-13: 978-1575862170.
  • Warren J. Ewens, and Gregory R. Grant. Statistical Methods in Bioinformatics, 2e. Springer, 2005. (Soft cover) ISBN 978-1-4419-2302-8. (Hard cover) ISBN 978-0-387-40082-2.
  • Dan E. Krane and Michael L. Raymer, Fundamental Concepts of Bioinformatics, Pearson, 2006.
  • T K Attwood, D J Parry-Smith, and Samiron Phukan, Introduction to Bioinformatics, Pearson, 2008.

Assignments

  • All problem codes are from Bioinformatics Stronghold in http://rosalind.info.
  • Submit an archive containing the following: (a) 1 directory per problem solved. Each directory should include the input dataset, code and output file. (b) A README file mentioning your name, registration number, rosalind username, the space and time complexity of your algorithm.
  • To be submitted by Monday, 9AM, through email to bioinformatics.nitk@gmail.com. Late submission will be penalized.
  • Note: Starting A3, the programming assignments are to be executed in teams of two.
No.Problems to Solve Submission Date
A1DNA, RNA, REVC, FIB, GC, HAMM, IPRB, PROT. 5th Jan
A2SUBS, CONS, GRPH, IEV, LCSM, LIA, MPRT, MRNA. 12th Jan
A3ORF, PERM, PRTM, REVP, SPLC, LEXF, LGIS, LONG, PMCH, PPER, PROB, SIGN.19th Jan
A4SSEQ, TRAN, TREE, CAT, CORR, INOD, KMER, KMP, LCSQ, LEXV, MMCH, PDST.27th Jan
A5REAR, RSTR, SSET, ASPC, EDIT, EVAL, MOTZ, NWCK, SCSP, SETO, SORT, SPEC.2nd Feb
A6TRIE, CONV, CTBL, DBRU.9th Feb
Midsem Break

Class Lectures

Most lecture notes are derived from Jones and Pevzner's slides from the Bioinformatics Algorithms textbook webpage.

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