Genome Structure & Evolution
Basics
DNA
Double Helix
Histones
Nucleosomes
Coils
Supercoils
Chromatin (Eu/ Hetero)
Chromosomes
Gene Maping
Cytogenic
Linkage
Physical
Sequencing
Shotgun Sequencing & Metagenomics
Bioinformatics
DNA Databases
National Center for Biotechnology Information (GenBank / BLAST)
European Molecular Biology Laboratory
DNA Data Bank of Japan
Beijing Genome Institute
Applications
DNA Sequence Comparisons (BLAST)
Protein Sequence Prediction
Protein Sequence to 3D modeling
Protein Domain Comparisons
Protein Domain Function Database
DNA / Protein Phylogenetic Relationships
Gene Annotations
See Functional Analysis under Biotechnology
Protein  mRNA  cDNA  Expressed Sequence Tag Library
Gene to Gene Comparisons
Interspecies Comparisons
Systems Approach
Developmental tracking of gene expression
Gene to gene relationships (epistasis, polygenic traits, pleitropy)
Gene to environment interactions (epistasis, signal transduction))
cDNA vs. DNA comparison for identification of active genes
Above vs. gene mapping (Linkage; Physical; Cytogenic; Sequencing; Coiling)
Proteomes & Protein Relationship Analysis
Examples
Knock-Out Pairs Studies
Protein Factor Studies
Gene Chip & Medical Applications
Genome Structure
Interspecies Comparison Studies
Size
Number
Gene Density
Functional RNA products (tRNA; snRNA; srpRNA; mRNA; rRNA) (<1.5%)  Alternative Splicing
Introns (also includes miRNA & siRNA) (5%)
Repetitive DNA (>95%)
Functions:
Possible ties to chromosome structuring & Protection (STRs)
Speeding up of variation (STRs; Transposable Elements)
Crossing over control (Transposable Elements)
Gene expression control (Transposable Elements: Gene Promotion/Inhibition; Polymerase Inhibition))
Amplification Errors (Transposable Elements; Large Sequence Duplications)
DNA Copy Errors (STRs; Large Sequence Duplications)
Evolutionary process (All; i.e.: Tranposable Elements & Exon Shuffling)
Types:
Unique Non Coding DNA (Pseudogenes + miRNA & siRNA) (15%)
Transposable Elements (>50%)
Coding & Non-Coding
Vast majority does not Productive Functional or Useful Protein (Normal Cellular Functions)
Most of Repetitive DNA
Transposition Recognition Sequence
Defunct Transposable Elements
DNA Aggregations & Inter-Chromosomal Exchange
Transposons & Retro transposons Mechanisms
Amplification (Duplication / Transposition to Active Promoter Box)
Non-Homologue pairing due to transposable element relationships
Examples
Alu  RNA of Uknown Function (300 bases)
Line-1 or L1 (6500)
Human genome only
RNA polymerase inhibition sequences
Neuron development
Large Sequence Duplications (5-6%)  10-300K bases
May include functional genes
Simple Sequence DNA (3%)
<500 bases; most <15;
2-5 = short tandem repeats
Telomere / centromere regions
Multigene Families (in higher level eukaryotes, this is the majority of 1.5% of coding genes)
Identical or nearly identical DNA
rRNA family
Globins
Gene Change & Evolution
Polyploidy & Variation (Protection from Mutation Problems while accelerating variation)
Chromosome fusion & splitting
Interspecies chromosomal analysis can be used as evolutionary relationship & timeline building mechanism
Chromosomal Rearrangement & Speciation
Duplication & Translocations
Errors During Meiosis Homologue Pairing (Transposable Elements)
Slippage during DNA synthesis
Protein Domain Analysis & Evidence of Exon Duplication & Shuffling in the Evolution of Genes
Genome Analysis & Philogenetics
Interspecies Comparisson
Distant
Domain Creation
Similarity in Life
Related
Gene / Phenotype Comparisons
Genome Mapping Acceleration
Human / Chimp Comparison
Clues about mental development
More duplications & exon shuffling in humans
Alu elements in humans
Provirus in chimps
Faster evolving human genes (transposable elements)
Brain size
Transciption Factors & Other regulatory genes (i.e.: FOXP2 vocalization gene)
Within Species
Short Tandem Repeats & Restriction Length Polymorphisms
Single Nucleotide Polymorphisms (100-300 bases)
Copy-Number Variant
Migration & “Race” Analysis
Developmental Process Comparison
Conservation of Developmental Genes Among Mammals
Homeobox (Hox Genes)
Animal vs. Plant Development