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12.Genomics and Bioinformatics.pdf

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Department
Biology (Sci)
Course
BIOL 200
Professor
Richard Roy
Semester
Fall

Description
Naveen Sooknanan McGill Fall 2011 Genomics and Bioinformatics: Genomics involves the sequencing pieces of DNA within a genome (particularly the human genome) and mapping the location of genes and other genomic entities  This mapping is called annotation  To this day, we are still trying to figure out the exact number of genes within the human genome Many different branches of genomics have arisen during the “-omics” era:  Functional genomics is the study of annotations  Proteomics is the study of gene products (such as proteins)  Evolutionary genomics has recently developed over the past 3-4 years and studies evolutionary trends and patters with respect to the genome  Transcriptomics look at the gene during various points in development  Phenomics looks at changes to the genes with given phenotypes  Other fields exist, such as: spliceomics, glycomics, metabolomics, lipidomics, kinomics, neuromics, predictomics o Getting to the point where every field has its own “-omics” The first genome sequences was the Epstein-Barr virus in 1984, because it has a very small genome, and since then, DNA has been sequences from 1000s of different, more complex organisms.  Mammalian sequencing is much more complex because of a much larger genome  Over 1700 genomes sequences by 2011 Various viruses and bacteria have been sequences fro obvious purposes, such as the influenza virus and Yersinia pestis (bubonic plague). Sequences have also been found that are from organisms which we now refer to as model organisms:  Yeast is very easy to sequence because it has one of the smallest eukaryotic genomes  Zebrafish are important in research into the nervous system  Roundworm, mice, fruit fly and plants are also model organisms There are over 600 completed and ongoing projects  Chimpanzees have not been fully sequences, as with humans  Sea squirts have been completely sequenced, and are useful for muscle development research  Barley and grape genomes have been sequences for beer and wine production  9 banded armadillo, a carrier of leprosy, have been sequenced  The elephant’s genome has been sequences o Note the size of the organism is not proportional to the size of its genome  A type of beetle that carries Chargoff’s disease has been sequenced 1gap gap gap gap gap gapNaveen Sooknanan McGill Fall 2011 Genomics can be seen as the piecing together of the world’s largest jigsaw puzzle. However, there are no visual patterns or algorithms that can be used for the genome, they all must be deciphered from random coding of A, C, T and G. A classic method of DNA sequencing is called shotgun sequencing, where the genome is blasted into 1000s of overlapping fragments by a process called mechanical shearing.  When these fragments are placed in the presence of a template strand, complementary base pairing occurs between the fragments and the template, but also between overlapping fragments  This binding of fragments one on top of the other creates a stair looking structure known as a tiling path o This creates continuous sequences known as contigs with gaps in-between. These gaps cannot be bridged for many technical reasons With many sequences, it is possible to piece together various contigs with perfect matches in overlapping fragments to produce the entire genome sequence. Nowadays, this technology (normal dideoxy DNA sequencing) is considered slow and out-dated as many new technologies have been invented by various bioinformatics companies.  Roche 454 pyrosequencing and Illumina Hisequencing are two examples of next generation sequencing methods by two different companies o These are sued in current genome projects and speed up the process by many orders of magnitude  These technologies are also getting cheaper and cheaper to use making them more accessible Roche 454 pyrosequencing has a very similar procedure to that of oligonucleotide synthesis. It involves the immobilization of a substrate onto a bead which are immobilized in bigger wells  Starting with the entire genome, mechanical shearing occurs to tear the genome into more manageable fragments  These fragments are then denatured (forming ssDNA) and are attached to attachments segments  These segments then interact with a molecule (bead) within a well  The bead quickly accumulated many more DNA fragments and are immobilized in wells within a test plate  Reagents are then added in a stepwise manner 2DNAn dNTPs merase DNA PP sulfurylase APS PPi sulfate ATP Luciferase luciferin +ATP oxyluciferin light C G IT A DNAn dNTPs merase DNA PP sulfurylase APS PPi sulfate ATP Luciferase luciferin +ATP oxyluciferin light C G IT ANaveen Sooknanan McGill Fall 2011 Pyrosequencing requires many typical reagents we have seen before, such as a template, primers, dNTPs and DNA polymerase, but also requires new reagents:  ATP sulfurylase  Adenosine 5’ phosphosulfate (APS)  Luciferase, which is responsible for the glowing of fireflies, and luciferin, which is required in this glowing reaction  Apy
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