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User:Mattb112885/Books/Bioinformatics (draft)

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Bioinformatics

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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