Genotype

http://www.howstuffworks.com/dna-evidence.htm

DNA Fingerprinting
DNA Fingerprinting is a way of identifying a specific individual, rather than simply identifying a species or some particular trait. DNA fingerprinting uses a specific type of DNA sequence, known as a microsatellite, to make identification much easier.

• All of the DNA sections are contained in every cell, any piece of a person's body, from a strand of hair to a skin follicle to a drop of blood, may be used to identify them using DNA fingerprinting.
• Every organism has its individual's unique sequence of DNA base pairs determined by exposing a sample of the organism’s DNA to molecular probes.
• Large regions of our DNA that do not consist of genes and appear to serve no useful purpose.
• Some orders of DNA are repeated thus making it easier for the scientists.
• Patterns are obtained that reflects different numbers of repeats in different individuals; the length of a particular DNA fragment is a function of the number of repeats present.
• Patterns are analyzed to get a certain probability of a match.


http://departments.oxy.edu/biology/Stillman/bi221/102700/notes.htm


http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/R/RFLPs.html

DNA sequencing of Ribosomal RNA Gene
DNA sequencing is the determination of the precise sequence of nucleotides in a sample of DNA.

• DNA sequencing has provided a new approach for studying evolutionary relationships, since :
- all organisms have a genome
- the genes that code for vital cellular functions are conserved to are markable degree through evolutionary time

• To carry out the sequencing of the organisms, scientists cut the DNA up into short fragments, sequenced these fragments simultaneously, and then assembled the entire genome by using sophisticated computer techniques to match the fragments to each other.

• DNA sequencing is also dependent on our ability to use gel electrophoresis to separate strands of DNA that differ in size by as little as one base pair.

• The gene most commonly used for this codes for the RNA in the small subunit (SSU) of the ribosome (16s rRNA)

• 16s rRNA acts like one have of two pieces of Velcro, any genes left over from matching in a given sample can be attributed to genes from previously unknown organisms.

• Some regions of this 16S rRNA are highly conserved in all organisms, whereas other regions are more variable.


Extracted from: http://www.nucleics.com/DNA_sequencing_tools/DNA_sequencing_tools.html


Extracted from: http://psychology.wikia.com/wiki/Evolution


Amino Acid Sequencing
• Comparison of amino acid sequences from proteins of different organisms is used to determine the similarity in the DNA sequences.

• Determining what conformation it adopts and whether it is complexed with any non-peptide molecules.

• The two major direct methods of protein sequencing are mass spectrometry and the Edman degradation reaction. It is also possible to generate an amino acid sequence from the DNA or mRNA sequence encoding the protein.

• Sequence information has been successfully applied to unveil structure, function, and evolutionary relationships.

• To understand the functional roles or structure families of proteins, a lot of computational methods have been developed to classify protein sequences and detect remote homology based on their sequence similarity.



　

Extracted From: http://www.mcgill.ca/sheldon/pep_seq
　
Protein Pattern Analysis
• Sequence of an uncharacterised protein translated from genomic sequences is too distantly related to any protein of known function by overall sequence alignment, but the protein function can be identified by the occurrence in its sequence of regions resembling a known functional site or a conserved protein family fragment.

• The result of analysis is set of matches with pattern or pattern portion.

• Proteins are the product of its genes and each species is expected to produce a set of unique proteins.

• Protein profiles are obtained by Polyacrylamide gel electrophoresis (PAGE) where different proteins migrate through the gel at different rate depending on their size and charge