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