Genome Project - PPT, Biotechnology, IBT, Semester, Engineering Biotechnology Engineering (BT) Notes | EduRev

Biotechnology Engineering (BT) : Genome Project - PPT, Biotechnology, IBT, Semester, Engineering Biotechnology Engineering (BT) Notes | EduRev

 Page 1


Genome project 
?Aim - to determine the complete genome 
sequence of an organism (an animal, a plant, a 
fungus, a bacterium, an archaean, a protist or a 
virus).  
 
?The genome sequence-to determine the DNA 
sequences for each of the chromosomes in an 
organism. eg.  
a)bacteria, which usually have just one 
chromosome, a genome project will aim to map 
the sequence of that chromosome.  
 
b)Humans have 22 pairs of autosomes and 2 sex 
chromosomes,so genome project will aim to map 
sequence of 46 chromosomes in order to 
represent the complete genome. 
   
Page 2


Genome project 
?Aim - to determine the complete genome 
sequence of an organism (an animal, a plant, a 
fungus, a bacterium, an archaean, a protist or a 
virus).  
 
?The genome sequence-to determine the DNA 
sequences for each of the chromosomes in an 
organism. eg.  
a)bacteria, which usually have just one 
chromosome, a genome project will aim to map 
the sequence of that chromosome.  
 
b)Humans have 22 pairs of autosomes and 2 sex 
chromosomes,so genome project will aim to map 
sequence of 46 chromosomes in order to 
represent the complete genome. 
   
Contents 
? 1 Genome assembly  
?1.1 Assembly software 
 
? 2 Genome annotation 
 
? 3 When is a genome project 
finished? 
 
? 4 Historical and technological 
perspectives  
Page 3


Genome project 
?Aim - to determine the complete genome 
sequence of an organism (an animal, a plant, a 
fungus, a bacterium, an archaean, a protist or a 
virus).  
 
?The genome sequence-to determine the DNA 
sequences for each of the chromosomes in an 
organism. eg.  
a)bacteria, which usually have just one 
chromosome, a genome project will aim to map 
the sequence of that chromosome.  
 
b)Humans have 22 pairs of autosomes and 2 sex 
chromosomes,so genome project will aim to map 
sequence of 46 chromosomes in order to 
represent the complete genome. 
   
Contents 
? 1 Genome assembly  
?1.1 Assembly software 
 
? 2 Genome annotation 
 
? 3 When is a genome project 
finished? 
 
? 4 Historical and technological 
perspectives  
1 Genome assembly 
?Genome assembly refers to the process of 
taking a large number of short DNA sequences, 
all of which were generated by a shotgun 
sequencing project, and putting them back 
together to create a representation of the 
original chromosomes from which the DNA 
originated. 
 
?Genome assembly is a very difficult 
computational problem, because many 
genomes contain large numbers of identical 
sequences, known as repeats. These repeats 
can be thousands of nucleotides long, and 
some occur in thousands of different locations, 
especially in the large genomes of plants and 
animals  
 
 
Page 4


Genome project 
?Aim - to determine the complete genome 
sequence of an organism (an animal, a plant, a 
fungus, a bacterium, an archaean, a protist or a 
virus).  
 
?The genome sequence-to determine the DNA 
sequences for each of the chromosomes in an 
organism. eg.  
a)bacteria, which usually have just one 
chromosome, a genome project will aim to map 
the sequence of that chromosome.  
 
b)Humans have 22 pairs of autosomes and 2 sex 
chromosomes,so genome project will aim to map 
sequence of 46 chromosomes in order to 
represent the complete genome. 
   
Contents 
? 1 Genome assembly  
?1.1 Assembly software 
 
? 2 Genome annotation 
 
? 3 When is a genome project 
finished? 
 
? 4 Historical and technological 
perspectives  
1 Genome assembly 
?Genome assembly refers to the process of 
taking a large number of short DNA sequences, 
all of which were generated by a shotgun 
sequencing project, and putting them back 
together to create a representation of the 
original chromosomes from which the DNA 
originated. 
 
?Genome assembly is a very difficult 
computational problem, because many 
genomes contain large numbers of identical 
sequences, known as repeats. These repeats 
can be thousands of nucleotides long, and 
some occur in thousands of different locations, 
especially in the large genomes of plants and 
animals  
 
 
Shotgun Sequencing Method (so named as genome is broken into small pieces as if it 
had been blasted with shotgun) 
 
    All the DNA from a source (usually a single organism, anything from a bacterium to 
a mammal) is first fractured into millions of small pieces.  
 
 
 
     These pieces are then "read" by automated sequencing machines, which can read 
up to 900 nucleotides or bases at a time. (The four bases are adenine, guanine, 
cytosine, and thymine, represented as AGCT.) 
 
 
 
 
    A genome assembly algorithm works by taking all the pieces and aligning them to 
one another. 
 
 
     
   Detecting all places where two of the short sequences, or reads, overlap.  
 
 
 
   These overlapping reads can be merged together, and the process continues. 
Page 5


Genome project 
?Aim - to determine the complete genome 
sequence of an organism (an animal, a plant, a 
fungus, a bacterium, an archaean, a protist or a 
virus).  
 
?The genome sequence-to determine the DNA 
sequences for each of the chromosomes in an 
organism. eg.  
a)bacteria, which usually have just one 
chromosome, a genome project will aim to map 
the sequence of that chromosome.  
 
b)Humans have 22 pairs of autosomes and 2 sex 
chromosomes,so genome project will aim to map 
sequence of 46 chromosomes in order to 
represent the complete genome. 
   
Contents 
? 1 Genome assembly  
?1.1 Assembly software 
 
? 2 Genome annotation 
 
? 3 When is a genome project 
finished? 
 
? 4 Historical and technological 
perspectives  
1 Genome assembly 
?Genome assembly refers to the process of 
taking a large number of short DNA sequences, 
all of which were generated by a shotgun 
sequencing project, and putting them back 
together to create a representation of the 
original chromosomes from which the DNA 
originated. 
 
?Genome assembly is a very difficult 
computational problem, because many 
genomes contain large numbers of identical 
sequences, known as repeats. These repeats 
can be thousands of nucleotides long, and 
some occur in thousands of different locations, 
especially in the large genomes of plants and 
animals  
 
 
Shotgun Sequencing Method (so named as genome is broken into small pieces as if it 
had been blasted with shotgun) 
 
    All the DNA from a source (usually a single organism, anything from a bacterium to 
a mammal) is first fractured into millions of small pieces.  
 
 
 
     These pieces are then "read" by automated sequencing machines, which can read 
up to 900 nucleotides or bases at a time. (The four bases are adenine, guanine, 
cytosine, and thymine, represented as AGCT.) 
 
 
 
 
    A genome assembly algorithm works by taking all the pieces and aligning them to 
one another. 
 
 
     
   Detecting all places where two of the short sequences, or reads, overlap.  
 
 
 
   These overlapping reads can be merged together, and the process continues. 
 
 
 
 
 
 
 
Assembly software 
 
?Phred/Phrap by Phil Green. 
 
?AMOS (A Modular Open Source Assembler) – This was initiated 
at Institute for Genomic Research by Steven Salzberg, Mihai 
Pop and Art Delcher, who are now at the university of Maryland. 
 
?Celera Assembler developed by Gene Myers, Granger Sutton, 
Art Delcher and others at Celera Genomics. 
 
?Arachne Assembler by Serafim Batzoglou now at Stanford 
University. 
 
?Short Oligonucleotide Analysis Package developed by BGI for 
de novo assembly of human-sized genomes, alignment, SNP 
detection, resequencing, indel finding, and structural variation 
analysis  
    
 
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