Genomic Perl : from bioinformatics basics to working code

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