The Central Dogma -- DNA and RNA -- Chromosomes -- Proteins -- The Central Dogma -- Transcription and Translation in Perl -- RNA Secondary Structure -- Messenger and Catalytic RNA -- Levels of RNA Structure -- Constraints on Secondary Structure -- RNA Secondary Structures in Perl -- Counting Hydrogen Bonds -- Folding RNA -- Comparing DNA Sequences -- DNA Sequencing and Sequence Assembly -- Alignments and Similarity -- Alignment and Similarity in Perl -- Predicting Species: Statistical Models -- Perl Subroutine Libraries -- Species Prediction in Perl -- Substitution Matrices for Amino Acids -- More on Homology -- Deriving Substitution Matrices from Alignments -- Substitution Matrices in Perl -- The PAM Matrices -- PAM Matrices in Perl -- Sequence Databases -- FASTA Format -- GenBank Format -- GenBank's Feature Locations -- Reading Sequence Files in Perl -- Object-Oriented Programming in Perl -- The SimpleReader Class -- Hiding File Formats with Method Inheritance -- Local Alignment and the BLAST Heuristic -- The Smith-Waterman Algorithm -- The BLAST Heuristic -- Preprocessing the Query String -- Scanning the Target String -- Implementing BLAST in Perl -- Statistics of BLAST Database Searches -- BLAST Scores for Random DNA -- BLAST Scores for Random Residues -- BLAST Statistics in Perl -- Interpreting BLAST Output -- Multiple Sequence Alignment I -- Extending the Needleman-Wunsch Algorithm -- NP-Completeness -- Alignment Merging: A Building Block for Heuristics -- Merging Alignments in Perl -- Finding a Good Merge Order.

This introduction to computational molecular biology will help programmers and biologists learn the skills they need to start work in this important, expanding field. The author explains many of the basic computational problems and gives concise, working programs to solve them in the Perl programming language. With minimal prerequisites, the author explains the biological background for each problem, develops a model for the solution, and then introduces the Perl concepts needed to implement the solution. The book covers pairwise and multiple sequence alignment, fast database searches for homologous sequences, protein motif identification, genome rearrangement, physical mapping, phylogeny reconstruction, satellite identification, sequence assembly, gene finding, and RNA secondary structure. The author focuses on one or two practical approaches for each problem rather than an exhaustive catalog of ideas. His concrete examples and step-by-step approach make it easy to grasp the computational and statistical methods, including dynamic programming, branch-and-bound optimization, greedy methods, maximum likelihood methods, substitution matrices, BLAST searching, and Karlin-Altschul statistics.