User:Mattb112885/Books/Bioinformatics (draft)

Bioinformatics

 * Intro
 * Bioinformatics


 * Sequence Alignment
 * Sequence alignment - Identification of the optimal alignment between sequences that maximizes their similarity
 * Needleman-wunsch algorithm - A global alignment algorithm guaranteed to find the optimal solution
 * Smith–Waterman algorithm - A local alignment algorithm guaranteed to find the optimal solution
 * BLAST - A local alignment algorithm that employs heuristics to speed up the search at the cost of possibly not finding the optimum
 * Multiple sequence alignment - Alignment of more than two proteins
 * List_of_sequence_alignment_software


 * Multiple sequence alignment and phylogenetics
 * Phylogenetics - The analysis of gene phylogenies that can be generated from multiple sequence alignments
 * Neighbor joining - A technique for making a phylogenetic tree
 * Maximum parsimony - A technique for making a phylogenetic tree
 * Minimum evolution - A technique for making a phylogenetic tree
 * Maximum likelihood - A technique for making a phylogenetic tree
 * Gene duplication - A phenomena that can be detected by examination of phylogenetic trees
 * Horizontal gene transfer - A phenomena that can be detected by comparing a reference phylogeny with a history of particular protein families.
 * Long branch attraction - A common problem that can occur when making a phylogenetic tree, making the resulting topology incorrect
 * List of phylogenetics software - Software to make phylogenetic trees
 * List_of_phylogenetic_tree_visualization_software - Software to visualize phylogenetic trees


 * Genomics- sequencing and assembly
 * Genomics
 * DNA sequencing
 * Full genome sequencing
 * Sequence assembly


 * Transcriptomics- RNA Expression and Regulation
 * Transcriptome
 * RNA-Seq
 * DNA microarray
 * RNA splicing
 * Non-coding RNA
 * Gene regulatory network


 * Proteomics
 * Proteomics
 * Protein–protein interaction
 * Posttranslational modification


 * Data Sources
 * Biological database
 * List of biological databases