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Bioinformatics Algorithms and Perl Programming
Alignment Basics, Local and Global Alignment, DOT Matrix Analysis, Scoring System, Evolutionary Matrices (PAM, BLOSUM), PSSM, Dynamic Programming: Smith-Waterman and Needleman-Wunsch Algorithms, BLAST & FASTA Algorithms, Statistical Significance, PSI & PHI Blast.
MSA Basics, MSA Scoring: Entropy & Sum of Pairs Method, Multi dimensional Dynamic Programming and Progressive Alignment Method, ClustalW/X tool.
The phylogeny problem, Tree Basics & Topology, Ultrametric property, Tree Reconstruction Methods (UPGMA, NJ, Parsimony & Maximum Likelihood), Boostrapping,
Perl variables and Data types (Scalar, List, Array and Hash), Default variables, Conditional Expressions, Iterations, Subroutines, File handling, Regular expressions, References, Anonymous data types, Perl-CGI, Perl Modules and Packages, basic arithmetic calculation, string function, mathematical and time function
OOPs Concept, BioPerl Module, Object & Classes, Implementing Bioperl Modules, CPAN Library.
1. Ivan Bayross. “HTML, DHTML, Javascript, PERL CGI”, BPB Publications. 2. James D.Tisdall. “Beginning Perl for Bioinformatics”. O’Rilley publication, 2001. 3. David Mount. “Bioinformatics: sequence and genome analysis”. Cold springer harbour press, 2004. 4. Gross LJ, Sung Wing-Kin et al. “Algorithms in Bioinformatics, A Practical Introduction”. Chapman and Hall,2009
1. R. Durbin, S. Eddy, A. Krogh, G. Mitchison. “Biological Sequence Analysis – Probabilistic Models of Proteins and Nucleic acids”. Cambridge University Press,1998. 2. Tom Phoenix, Randal L. Schwartz. “Learning Perl”. O-Reilly publication,2001. 3. Sriram Srinivasan. “Advanced Perl Programming”. O-Reilly publication,1997.
