Bio Informatics - Genome Assembly
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A genome assembly is an attempt to accurately represent an entire genome sequence from a large set of very short DNA sequences.
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Genomics
Genomics is the field of studying genomes through techniques like DNA sequencing and bioinformatics. It aims to understand genome content, organization, function, and evolution. Genomics has two main areas - structural genomics determines genome sequence and organization, while functional genomics studies gene function. A third area, comparative genomics, compares genomes across species. Genomics research has contributed to human health, agriculture and other fields by providing gene sequences. Comparing genome sequences is also improving understanding of evolution and life's history.
Gene mapping and sequencing
This document discusses gene mapping and sequencing. It begins by defining genomics and genetic markers such as RFLP, SSLP, and SNP that are used to track inheritance. Gene mapping involves determining the locus and distance between genes on chromosomes, which is important for diagnosing genetic diseases. There are two main types of gene mapping: linkage mapping which measures recombination frequency to determine if genes are linked, and physical mapping which precisely locates DNA sequences on chromosomes using techniques like fluorescence in situ hybridization. The document also discusses methods for gene sequencing, including Sanger sequencing and Maxam-Gilbert sequencing, as well as newer techniques like shotgun sequencing and Illumina sequencing.
Gene expression & its regulation.
This presentation provide knowledge about Gene Expression & its regulation in brief.
i hope it gives some information about gene expression in your academic time.
In this presentation mentioned - Lac Operon and its expressor.
Gene mapping | Genetic map | Physical Map | DNA Data Analysis (upgraded)
Genes are useful markers but not ideal.
Mapped feature that are not genes are called DNA markers.
DNA markers must have at least two alleles to be useful.
DNA sequence features that satisfy this requirement are-
– Restriction Fragment Length Polymorphism (RFLP)
Southern hybridization
PCR
– Simple Sequence Length Polymorphism (SSLP)
– Single Nucleotide Polymorphism (SNP)
Mapping- determining the location of elements with in a genome, with respect to identifiable land marks.
Gene mapping describes the methods used to identify the locus of a gene and the distances between genes.
In simple mapping of genes to specific locations on chromosomes.
Two types
Genetic map
Physical Map
They are useful in predicting results of dihybrid and trihybrid crosses.
It allows geneticists to understand the overall complexity and genetic organization of a particular species.
Identify genes responsible for diseases.
Identify genes responsible for traits.
genetic maps are useful from an evolutionary point of view.
Gene mapping methods
Gene mapping involves determining the physical location of genes on chromosomes. There are two main types of gene mapping: genetic mapping and physical mapping. Genetic mapping uses genetic techniques like linkage analysis to construct maps showing relative gene positions based on recombination frequencies. Physical mapping uses molecular biology techniques to directly examine DNA and determine absolute positions of genes and sequences. Key methods in physical mapping include restriction mapping, fluorescence in situ hybridization (FISH), and sequence tagged site (STS) mapping. Gene mapping is important for understanding genetic diseases and developing gene therapy methods.
Sts
Sequence tagged sites (STSs) are short DNA sequences that can be used as genetic markers. STSs were introduced in 1989 as a way to map genes along chromosomes using PCR. They serve as landmarks on physical maps of genomes. STSs are mapped by breaking genomes into fragments, replicating the fragments in bacterial cells to create libraries, and using PCR to determine which fragments contain STSs. Different types of STS markers include microsatellites, SCARs, CAPs, and ISSRs, each of which has distinct characteristics and applications in genetic mapping, population studies, and other areas.
Molecular marker and gene mapping
Molecular marker and gene mapping ppt
properties of molecular marker
types of molecular marker
mapping
genetic mapping
application of molecular marker
Physical maps and their use in annotations
This document discusses physical maps and their use in genome annotation. It provides information on several key topics:
- Physical maps show the relative positions of genes on chromosomes, similar to a topological map of a country. They are created by identifying DNA fragments using genetic markers or restriction enzymes.
- Genetic mapping was first described in 1911 and applied to humans in the 1950s. Whole genome maps were generated by the mid-1990s using improved techniques.
- Physical mapping involves cloning chromosomal fragments, determining their sizes and relative locations to construct a map. Pulsed-field gel electrophoresis and fluorescence-activated cell sorting are used to isolate individual chromosomes.
- Contigs are assembled from overlapping cloned fragments to
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Genomics
Genomics is the field of studying genomes through techniques like DNA sequencing and bioinformatics. It aims to understand genome content, organization, function, and evolution. Genomics has two main areas - structural genomics determines genome sequence and organization, while functional genomics studies gene function. A third area, comparative genomics, compares genomes across species. Genomics research has contributed to human health, agriculture and other fields by providing gene sequences. Comparing genome sequences is also improving understanding of evolution and life's history.
Gene mapping and sequencing
This document discusses gene mapping and sequencing. It begins by defining genomics and genetic markers such as RFLP, SSLP, and SNP that are used to track inheritance. Gene mapping involves determining the locus and distance between genes on chromosomes, which is important for diagnosing genetic diseases. There are two main types of gene mapping: linkage mapping which measures recombination frequency to determine if genes are linked, and physical mapping which precisely locates DNA sequences on chromosomes using techniques like fluorescence in situ hybridization. The document also discusses methods for gene sequencing, including Sanger sequencing and Maxam-Gilbert sequencing, as well as newer techniques like shotgun sequencing and Illumina sequencing.
Gene expression & its regulation.
This presentation provide knowledge about Gene Expression & its regulation in brief.
i hope it gives some information about gene expression in your academic time.
In this presentation mentioned - Lac Operon and its expressor.
Gene mapping | Genetic map | Physical Map | DNA Data Analysis (upgraded)
Genes are useful markers but not ideal.
Mapped feature that are not genes are called DNA markers.
DNA markers must have at least two alleles to be useful.
DNA sequence features that satisfy this requirement are-
– Restriction Fragment Length Polymorphism (RFLP)
Southern hybridization
PCR
– Simple Sequence Length Polymorphism (SSLP)
– Single Nucleotide Polymorphism (SNP)
Mapping- determining the location of elements with in a genome, with respect to identifiable land marks.
Gene mapping describes the methods used to identify the locus of a gene and the distances between genes.
In simple mapping of genes to specific locations on chromosomes.
Two types
Genetic map
Physical Map
They are useful in predicting results of dihybrid and trihybrid crosses.
It allows geneticists to understand the overall complexity and genetic organization of a particular species.
Identify genes responsible for diseases.
Identify genes responsible for traits.
genetic maps are useful from an evolutionary point of view.
Gene mapping methods
Gene mapping involves determining the physical location of genes on chromosomes. There are two main types of gene mapping: genetic mapping and physical mapping. Genetic mapping uses genetic techniques like linkage analysis to construct maps showing relative gene positions based on recombination frequencies. Physical mapping uses molecular biology techniques to directly examine DNA and determine absolute positions of genes and sequences. Key methods in physical mapping include restriction mapping, fluorescence in situ hybridization (FISH), and sequence tagged site (STS) mapping. Gene mapping is important for understanding genetic diseases and developing gene therapy methods.
Sts
Sequence tagged sites (STSs) are short DNA sequences that can be used as genetic markers. STSs were introduced in 1989 as a way to map genes along chromosomes using PCR. They serve as landmarks on physical maps of genomes. STSs are mapped by breaking genomes into fragments, replicating the fragments in bacterial cells to create libraries, and using PCR to determine which fragments contain STSs. Different types of STS markers include microsatellites, SCARs, CAPs, and ISSRs, each of which has distinct characteristics and applications in genetic mapping, population studies, and other areas.
Molecular marker and gene mapping
Molecular marker and gene mapping ppt
properties of molecular marker
types of molecular marker
mapping
genetic mapping
application of molecular marker
Physical maps and their use in annotations
This document discusses physical maps and their use in genome annotation. It provides information on several key topics:
- Physical maps show the relative positions of genes on chromosomes, similar to a topological map of a country. They are created by identifying DNA fragments using genetic markers or restriction enzymes.
- Genetic mapping was first described in 1911 and applied to humans in the 1950s. Whole genome maps were generated by the mid-1990s using improved techniques.
- Physical mapping involves cloning chromosomal fragments, determining their sizes and relative locations to construct a map. Pulsed-field gel electrophoresis and fluorescence-activated cell sorting are used to isolate individual chromosomes.
- Contigs are assembled from overlapping cloned fragments to
genome Mapping by pcr
The document discusses how polymerase chain reaction (PCR) has revolutionized the creation of molecular maps. PCR allows for the amplification of specific DNA sequences, enabling the use of DNA-based markers for mapping. These PCR-based markers include RAPDs, AFLPs, and STSs. Genetic maps show the relative order and distance of markers on chromosomes, while physical maps show the actual base pair distances. Both genetic and physical maps provide information about gene locations that can aid in understanding genomes and genetic diseases.
GENOMIC MAPPING:FISH(Fluorescent in situ hybridization )
Genomic mapping is a graphic representation of the arrangement of genes or DNA sequences on chromosome & used to identify and record the location of gene & distances between genes on chromosome.
There are mainly two kinds of genome maps are known : 1.Genetic or linkage maps & 2. Physical maps
Where Physical map provides detail of the actual physical distance between genetic markers, as well as the exact location of genes.
An example of Physical mapping is FISH. FISH is a powerful technique for detecting RNA or DNA sequences in cells, tissues & tumors
Chromosome walking
Chromosome walking is a method used to isolate and clone a particular gene or allele by using overlapping DNA fragments as probes to successively isolate flanking genomic clones. It involves constructing a genomic library, identifying a starting sequence fragment, using that as a probe to isolate an adjacent fragment, then using that new fragment as a probe to isolate the next overlapping fragment in a walking process. It has applications in analyzing genetically transmitted diseases and discovering single nucleotide polymorphisms, but can be slowed by repeated sequences and unclonable DNA regions.
Construction of physical mapping
Physical mapping involves determining the locations of identifiable landmarks on DNA molecules, such as restriction enzyme cutting sites or genes, and measuring their distances in base pairs. One physical mapping method is fluorescent in situ hybridization (FISH), which detects the positions of markers or genes on chromosomes by hybridizing fluorescent probes to chromosomal DNA on slides under a microscope. Another major approach is restriction fragment overlapping based physical mapping using bacterial artificial chromosomes (BACs). BAC-based physical mapping does not require chromosome slide preparation like FISH and can map hundreds or thousands of genes to contigs.
Molecular Markers
Dr. S. MANIKANDAN, M.Sc., Ph.D
Lecturer in Botany
Thiruvalluvar University Model Constituent College,
Tittagudi 606 106, Tamil Nadu, India.
Email id: drgsmanikandan@gmail.com
Gene mapping
Gene mapping determines the order and relative distances between genes on a chromosome. Genes that are close together are less likely to assort independently during meiosis due to crossover events between them. The chance of recombination between two genes is directly related to their physical distance apart, with one map unit equaling a 1% chance of recombination. Gene mapping methods use recombination frequencies observed between alleles in offspring to calculate the relative distances between genes. Common markers used for gene mapping include RFLPs, SNPs, and SSRs, which identify polymorphisms that can be traced during meiosis.
Genome assembly
This document discusses different methods for genome sequencing and assembly, including restriction enzyme fingerprinting, marker sequences, and hybridization assays. It focuses on using marker sequences like sequence-tagged sites (STS), expressed sequence tags (ESTs), untranslated regions (UTRs), and single nucleotide polymorphisms (SNPs) to map genomes. Large-insert cloning vectors like BACs and PACs can be used with restriction enzyme fingerprinting and FPC software to assemble contigs and map genomes at a large scale. Marker sequences provide a dense set of physical markers to build accurate physical maps of genomes.
Genetic and Physical map of Genome
Introduction
History
Genetic mapping
DNA Markers
Physical mapping
Importance
Drawback
Conclusion
References
uses genetic techniques to construct maps showing the positions of genes and other sequence features on a genome.
Genetic techniques include cross-breeding experiments or, in the case of humans, the examination of family histories (pedigrees).
Nucleic Acid Hybridisation & Gene Mapping
Nucleic acid hybridization can be used to identify particular DNA sequences using a nucleic acid probe. The technique takes advantage of DNA's property of complementary base pairing - if DNA is separated into single strands, the complementary strands will reform into double helices when conditions are right. A nucleic acid probe is a short, radioactively labelled single-stranded DNA or RNA molecule that binds to complementary nucleic acid sequences, allowing them to be identified. Genetic mapping uses genetic markers and recombination frequency during meiosis to locate genes on chromosomes and establish the relative distances between genes.
Genomic mapping, genetic mapping
Introduction
Genome mapping
History
Genetic mapping
Genetic markers
Linkage mapping
Recombination frequency
Physical mapping
Uses of genomic mapping
Limitation
References
Whole genome shotgun sequencing
Whole genome shotgun sequencing involves randomly breaking genomic DNA into small fragments, sequencing the fragments, and then reassembling the sequences using overlapping regions. The document outlines the history and procedure of shotgun sequencing. Genomic DNA is first fragmented, end-repaired, and size-selected into small, medium, and large fragments. Libraries are created for each size fragment and sequenced. A base caller filters poor calls and an assembler finds overlaps to generate continuous nucleotide sequences or contigs of the whole genome.
Genome mapping
Genetic mapping involves using genetic techniques like examining family histories or cross-breeding experiments to construct maps showing the positions of genes and other sequence features on a genome. Physical mapping uses molecular biology techniques to directly examine DNA molecules. The document discusses different types of genetic markers that can be used, including genes, RFLPs, SSLPs and SNPs. Genetic maps are useful for identifying genes responsible for diseases and traits, as well as applications in forensics, organ transplants, and authenticating consumer goods.
Mapping Techniques - Fluorescent in situ Hybridization(FISH) and Sequence Tag...
FISH is a fluorescent in situ hybridization technique that uses fluorescent probes to bind to specific DNA sequences on chromosomes, allowing their visualization under a microscope. It can be used to detect chromosomal abnormalities, assist with gene mapping, and study chromosomal structure. The procedure involves denaturing chromosomes and probes, hybridizing them, and fluorescent staining before examination. STS mapping similarly uses short, unique DNA sequences as markers that can be detected via PCR to map positions in the genome and identify polymorphisms useful for genetic analysis.
Genome mapping
Genetic mapping involves constructing maps that show the positions of genes and other sequences on a genome. It uses genetic techniques like cross-breeding experiments or examining family histories. Markers like genes, RFLPs, SSLPs, and SNPs are used in mapping. Genetic mapping is based on genetic linkage and inheritance. By determining the recombination frequency between markers, which is proportional to their distance apart, a genetic map can be constructed showing the relative positions of genes on chromosomes.
Lecture 2
1. Genetic linkage maps show the relative locations of DNA markers along chromosomes, while physical maps show the exact positions of genes and sequences.
2. Major methods for genetic mapping are RFLPs, microsatellites, and SNPs, while physical mapping uses restriction fingerprinting, chromosome walking, STS mapping, and FISH.
3. Gene mapping is useful for locating gene positions, estimating genetic risk, and has aided in fully sequencing genomes like yeast, worms, flies, mice, and humans.
Genome Mapping
Genetic and physical mapping are two categories of genome mapping methods. Genetic mapping uses genetic techniques like cross-breeding experiments to construct maps showing gene positions, while physical mapping uses molecular biology techniques to directly examine DNA molecules. DNA markers like RFLPs, SSLPs, and SNPs are now commonly used in genetic mapping as they are more abundant than genes. Physical mapping techniques include restriction mapping, fluorescent in situ hybridization (FISH), and sequence tagged site (STS) mapping. Genome mapping is important for locating disease genes, studying their sequences and proteins, and developing gene therapy methods.
Concept of genome mapping
This document discusses genome mapping and gene mapping. Genome mapping involves assigning DNA fragments to chromosomes to create a genetic map and guide for sequencing. There are two categories of mapping - genetic mapping using techniques like crossbreeding, and physical mapping which examines DNA directly. Gene mapping determines the order and distance between genes in map units and uses recombination frequencies to estimate distances. Mapping techniques like linkage analysis and using DNA markers like RFLPs, SSLPs, and SNPs help construct linkage maps of the genome.
Aflp (amplified fragment length polymorphism), alu
Alu PCR amplifies repetitive Alu elements in DNA using Alu-specific primers. The presence or absence of Alu insertions can be used for population genetics, forensics, and paternity testing. Alu elements are short, inter
Gene mapping and DNA markers
Gene mapping involves identifying the location of genes on chromosomes. It can help identify genes associated with inherited diseases. There are two main types of gene mapping: linkage mapping, which determines the relative distances between genes on a chromosome, and physical mapping, which measures distances in nucleotide bases. Gene mapping is done using various genetic markers, such as single nucleotide polymorphisms, microsatellites, and restriction fragment length polymorphisms. The goal is to better understand gene expression and regulation to help develop treatments and cures for genetic disorders.
Pcr based gene cloning
This document discusses PCR-based gene cloning and positional cloning. It describes how PCR allows for the amplification of specific DNA fragments in vitro using DNA polymerase. The key steps of PCR involve denaturation of DNA, annealing of primers, and extension of new DNA strands. Positional cloning is used to locate the position of disease-associated genes by using linkage analysis and mapping the chromosome region associated with the disease. Together, PCR and positional cloning techniques allow researchers to isolate and amplify individual gene sequences for further study.
CROP GENOME SEQUENCING
Two approaches (clone by clone & whole genome shotgun).
Types of DNA sequencing ( 1st, next and 3rd).
Crop genomes sequenced . (Example :Arabidopsis,Rice, Pigeon pea)
Genomic library
Genomic library and shotgun sequencing. It includes the topics about genomic library,construction method, its uses and applications, shotgun sequencing, difference between random and whole genome sequencing, its advantages and disadvantages etc.
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genome Mapping by pcr
The document discusses how polymerase chain reaction (PCR) has revolutionized the creation of molecular maps. PCR allows for the amplification of specific DNA sequences, enabling the use of DNA-based markers for mapping. These PCR-based markers include RAPDs, AFLPs, and STSs. Genetic maps show the relative order and distance of markers on chromosomes, while physical maps show the actual base pair distances. Both genetic and physical maps provide information about gene locations that can aid in understanding genomes and genetic diseases.
GENOMIC MAPPING:FISH(Fluorescent in situ hybridization )
Genomic mapping is a graphic representation of the arrangement of genes or DNA sequences on chromosome & used to identify and record the location of gene & distances between genes on chromosome.
There are mainly two kinds of genome maps are known : 1.Genetic or linkage maps & 2. Physical maps
Where Physical map provides detail of the actual physical distance between genetic markers, as well as the exact location of genes.
An example of Physical mapping is FISH. FISH is a powerful technique for detecting RNA or DNA sequences in cells, tissues & tumors
Chromosome walking
Chromosome walking is a method used to isolate and clone a particular gene or allele by using overlapping DNA fragments as probes to successively isolate flanking genomic clones. It involves constructing a genomic library, identifying a starting sequence fragment, using that as a probe to isolate an adjacent fragment, then using that new fragment as a probe to isolate the next overlapping fragment in a walking process. It has applications in analyzing genetically transmitted diseases and discovering single nucleotide polymorphisms, but can be slowed by repeated sequences and unclonable DNA regions.
Construction of physical mapping
Physical mapping involves determining the locations of identifiable landmarks on DNA molecules, such as restriction enzyme cutting sites or genes, and measuring their distances in base pairs. One physical mapping method is fluorescent in situ hybridization (FISH), which detects the positions of markers or genes on chromosomes by hybridizing fluorescent probes to chromosomal DNA on slides under a microscope. Another major approach is restriction fragment overlapping based physical mapping using bacterial artificial chromosomes (BACs). BAC-based physical mapping does not require chromosome slide preparation like FISH and can map hundreds or thousands of genes to contigs.
Molecular Markers
Dr. S. MANIKANDAN, M.Sc., Ph.D
Lecturer in Botany
Thiruvalluvar University Model Constituent College,
Tittagudi 606 106, Tamil Nadu, India.
Email id: drgsmanikandan@gmail.com
Gene mapping
Gene mapping determines the order and relative distances between genes on a chromosome. Genes that are close together are less likely to assort independently during meiosis due to crossover events between them. The chance of recombination between two genes is directly related to their physical distance apart, with one map unit equaling a 1% chance of recombination. Gene mapping methods use recombination frequencies observed between alleles in offspring to calculate the relative distances between genes. Common markers used for gene mapping include RFLPs, SNPs, and SSRs, which identify polymorphisms that can be traced during meiosis.
Genome assembly
This document discusses different methods for genome sequencing and assembly, including restriction enzyme fingerprinting, marker sequences, and hybridization assays. It focuses on using marker sequences like sequence-tagged sites (STS), expressed sequence tags (ESTs), untranslated regions (UTRs), and single nucleotide polymorphisms (SNPs) to map genomes. Large-insert cloning vectors like BACs and PACs can be used with restriction enzyme fingerprinting and FPC software to assemble contigs and map genomes at a large scale. Marker sequences provide a dense set of physical markers to build accurate physical maps of genomes.
Genetic and Physical map of Genome
Introduction
History
Genetic mapping
DNA Markers
Physical mapping
Importance
Drawback
Conclusion
References
uses genetic techniques to construct maps showing the positions of genes and other sequence features on a genome.
Genetic techniques include cross-breeding experiments or, in the case of humans, the examination of family histories (pedigrees).
Nucleic Acid Hybridisation & Gene Mapping
Nucleic acid hybridization can be used to identify particular DNA sequences using a nucleic acid probe. The technique takes advantage of DNA's property of complementary base pairing - if DNA is separated into single strands, the complementary strands will reform into double helices when conditions are right. A nucleic acid probe is a short, radioactively labelled single-stranded DNA or RNA molecule that binds to complementary nucleic acid sequences, allowing them to be identified. Genetic mapping uses genetic markers and recombination frequency during meiosis to locate genes on chromosomes and establish the relative distances between genes.
Genomic mapping, genetic mapping
Introduction
Genome mapping
History
Genetic mapping
Genetic markers
Linkage mapping
Recombination frequency
Physical mapping
Uses of genomic mapping
Limitation
References
Whole genome shotgun sequencing
Whole genome shotgun sequencing involves randomly breaking genomic DNA into small fragments, sequencing the fragments, and then reassembling the sequences using overlapping regions. The document outlines the history and procedure of shotgun sequencing. Genomic DNA is first fragmented, end-repaired, and size-selected into small, medium, and large fragments. Libraries are created for each size fragment and sequenced. A base caller filters poor calls and an assembler finds overlaps to generate continuous nucleotide sequences or contigs of the whole genome.
Genome mapping
Genetic mapping involves using genetic techniques like examining family histories or cross-breeding experiments to construct maps showing the positions of genes and other sequence features on a genome. Physical mapping uses molecular biology techniques to directly examine DNA molecules. The document discusses different types of genetic markers that can be used, including genes, RFLPs, SSLPs and SNPs. Genetic maps are useful for identifying genes responsible for diseases and traits, as well as applications in forensics, organ transplants, and authenticating consumer goods.
Mapping Techniques - Fluorescent in situ Hybridization(FISH) and Sequence Tag...
FISH is a fluorescent in situ hybridization technique that uses fluorescent probes to bind to specific DNA sequences on chromosomes, allowing their visualization under a microscope. It can be used to detect chromosomal abnormalities, assist with gene mapping, and study chromosomal structure. The procedure involves denaturing chromosomes and probes, hybridizing them, and fluorescent staining before examination. STS mapping similarly uses short, unique DNA sequences as markers that can be detected via PCR to map positions in the genome and identify polymorphisms useful for genetic analysis.
Genome mapping
Genetic mapping involves constructing maps that show the positions of genes and other sequences on a genome. It uses genetic techniques like cross-breeding experiments or examining family histories. Markers like genes, RFLPs, SSLPs, and SNPs are used in mapping. Genetic mapping is based on genetic linkage and inheritance. By determining the recombination frequency between markers, which is proportional to their distance apart, a genetic map can be constructed showing the relative positions of genes on chromosomes.
Lecture 2
1. Genetic linkage maps show the relative locations of DNA markers along chromosomes, while physical maps show the exact positions of genes and sequences.
2. Major methods for genetic mapping are RFLPs, microsatellites, and SNPs, while physical mapping uses restriction fingerprinting, chromosome walking, STS mapping, and FISH.
3. Gene mapping is useful for locating gene positions, estimating genetic risk, and has aided in fully sequencing genomes like yeast, worms, flies, mice, and humans.
Genome Mapping
Genetic and physical mapping are two categories of genome mapping methods. Genetic mapping uses genetic techniques like cross-breeding experiments to construct maps showing gene positions, while physical mapping uses molecular biology techniques to directly examine DNA molecules. DNA markers like RFLPs, SSLPs, and SNPs are now commonly used in genetic mapping as they are more abundant than genes. Physical mapping techniques include restriction mapping, fluorescent in situ hybridization (FISH), and sequence tagged site (STS) mapping. Genome mapping is important for locating disease genes, studying their sequences and proteins, and developing gene therapy methods.
Concept of genome mapping
This document discusses genome mapping and gene mapping. Genome mapping involves assigning DNA fragments to chromosomes to create a genetic map and guide for sequencing. There are two categories of mapping - genetic mapping using techniques like crossbreeding, and physical mapping which examines DNA directly. Gene mapping determines the order and distance between genes in map units and uses recombination frequencies to estimate distances. Mapping techniques like linkage analysis and using DNA markers like RFLPs, SSLPs, and SNPs help construct linkage maps of the genome.
Aflp (amplified fragment length polymorphism), alu
Alu PCR amplifies repetitive Alu elements in DNA using Alu-specific primers. The presence or absence of Alu insertions can be used for population genetics, forensics, and paternity testing. Alu elements are short, inter
Gene mapping and DNA markers
Gene mapping involves identifying the location of genes on chromosomes. It can help identify genes associated with inherited diseases. There are two main types of gene mapping: linkage mapping, which determines the relative distances between genes on a chromosome, and physical mapping, which measures distances in nucleotide bases. Gene mapping is done using various genetic markers, such as single nucleotide polymorphisms, microsatellites, and restriction fragment length polymorphisms. The goal is to better understand gene expression and regulation to help develop treatments and cures for genetic disorders.
Pcr based gene cloning
This document discusses PCR-based gene cloning and positional cloning. It describes how PCR allows for the amplification of specific DNA fragments in vitro using DNA polymerase. The key steps of PCR involve denaturation of DNA, annealing of primers, and extension of new DNA strands. Positional cloning is used to locate the position of disease-associated genes by using linkage analysis and mapping the chromosome region associated with the disease. Together, PCR and positional cloning techniques allow researchers to isolate and amplify individual gene sequences for further study.
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GENOMIC MAPPING:FISH(Fluorescent in situ hybridization )
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Mapping Techniques - Fluorescent in situ Hybridization(FISH) and Sequence Tag...
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Aflp (amplified fragment length polymorphism), alu
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Similar to Bio Informatics - Genome Assembly
CROP GENOME SEQUENCING
Two approaches (clone by clone & whole genome shotgun).
Types of DNA sequencing ( 1st, next and 3rd).
Crop genomes sequenced . (Example :Arabidopsis,Rice, Pigeon pea)
Genomic library
Genomic library and shotgun sequencing. It includes the topics about genomic library,construction method, its uses and applications, shotgun sequencing, difference between random and whole genome sequencing, its advantages and disadvantages etc.
THE human genome
Genomic sequencing allows researchers to determine the order of DNA nucleotides in whole genomes. There are two main approaches - hierarchical shotgun sequencing and whole genome shotgun sequencing. Hierarchical shotgun sequencing was used for the Human Genome Project. It involves first creating a physical map using markers like RFLPs, VNTRs, and STSs. The genome is then broken into large clones which are sequenced and assembled based on the physical map. Advances in genomic sequencing have led to sequencing of many important genomes like yeast, nematode, rice, fruit fly, and human. Genomic sequencing provides valuable information about gene structure and organization and aids in understanding genome function and evolution.
Synthesis of microbial genomes
This document summarizes techniques used for the synthesis of microbial genomes, including polymerase cycling assembly (PCA) and Gibson assembly. It provides details on the synthesis of several genomes, including:
1) The first synthetic genome of Mycoplasma genitalium in 2008 using 101 cassettes joined together.
2) The design and synthesis of a minimal bacterial genome of Mycoplasma mycoides, reduced from the original to 531 kb.
3) The chemical synthesis of Caulobacter ethensis-2.0, a minimized 1.76 Mb bacterial genome assembled in yeast.
4) The synthesis of an Escherichia coli genome with a recoded 61-codon
Shotgun and clone contig method
In shotgun sequencing the genome is broken randomly into short fragments (1 to 2 kbp long) suitable for sequencing. The fragments are ligated into a suitable vector and then partially sequenced. Around 400–500 bp of sequence can be generated from each fragment in a single sequencing run. In some cases, both ends of a fragment are sequenced. Computerized searching for overlaps between individual sequences then assembles the complete sequence.
Genomic library
Genomic libraries are collections of bacteria that have been engineered to contain the entire DNA of an organism. DNA from the organism is cut into fragments and inserted into cloning vectors like plasmids within bacteria. Together the bacteria hold the complete genome. Genomic libraries allow researchers to isolate and study specific DNA sequences using probes, map genomes, and clone DNA segments for various research purposes like genetic modification of crops. They are constructed by extracting, cutting, and ligating an organism's DNA into vectors within host bacteria. Different vectors have varying capacities to hold DNA fragments, ranging from plasmids at 15kb to yeast artificial chromosomes at up to 2,000kb.
2013 duke-talk
Digital normalization is a new technique for pre-filtering sequencing reads that helps address computational challenges in assembling genomes, transcriptomes, and metagenomes from non-model organisms. It works by discarding redundant reads to smooth coverage and eliminate the majority of errors. Three case studies showed its effectiveness: 1) Assembling the parasitic nematode H. contortus genome, 2) Assembling the lamprey transcriptome without a reference, and 3) Assembling two large soil metagenomes. Digital normalization enabled efficient assemblies and new biological insights in these difficult "weird" samples.
recumbinant DNA.pdf
Recombinant DNA technology allows for the cloning and manipulation of DNA. DNA is first isolated from an organism and cut with restriction enzymes. The cut DNA fragments are then inserted into cloning vectors like plasmids or phage lambda. These recombinant DNA molecules are introduced into host cells, where they can be replicated in large quantities. Libraries of cloned DNA fragments can be generated that represent entire genomes or individual chromosomes, enabling applications such as genetic mapping, DNA sequencing, and genetic engineering.
Genome Assembly copy
The genome assembly is simply the genome sequence produced after chromosomes have been fragmented, those fragments have been sequenced, and the resulting sequences have been put back together. Genome assembly has been metaphorically described as the process of assembling a jigsaw puzzle from the individual reads.
Genome assembly software (BySS, AMOS, Arapan-M, Arapan-S, Cortex, DNA Baser, DNAnexus etc.) combines the read into larger regions called contigs.
Dna assembly 2
This document describes a new method called DNA assembler that allows for the rapid assembly of entire biochemical pathways in a single step using in vivo homologous recombination in yeast. The method is demonstrated by assembling a 9 kb D-xylose utilization pathway (3 genes), an 11 kb zeaxanthin biosynthesis pathway (5 genes), and a 19 kb combined D-xylose and zeaxanthin pathway (8 genes), all with high efficiencies of 70-100%. DNA assembler represents an improvement over previous methods for pathway construction as it is faster, requires only simple DNA preparation and one-step yeast transformation, and can assemble larger pathways without limitations on restriction sites.
2013 UW Grad Conference
Talk given at University of Waterloo Biology Graduate Student Conference 2013. Won Outstanding Seminar Award.
Shotgun (2) metagenomics
Metagenomics is the study of microbial communities directly from environmental samples without isolating individual microbial strains. Next-generation sequencing allows researchers to sequence thousands of organisms in parallel from a sample. Metagenomic studies involve extracting DNA from a sample, fragmenting the DNA, and sequencing the fragments to determine the microbial diversity and genes present in the community. The Illumina sequencing workflow involves sample preparation through fragmentation and adaptor ligation, cluster generation by bridge amplification on a flow cell, sequencing by synthesis using fluorescently labeled nucleotides, and data analysis to assemble sequences and identify genes.
Genomiclibrary 151004020241-lva1-app6891
Genomic libraries contain DNA fragments representing an organism's entire genome. They are created through molecular cloning by isolating genomic DNA, fragmenting it, inserting the fragments into vectors, and introducing the vectors into bacteria. This collection of cloned DNA fragments comprises the genomic library and allows researchers to identify and study specific genes of interest. Shotgun sequencing is an alternative approach that involves randomly fragmenting genomic DNA and determining the nucleotide sequence of each fragment to reconstruct the full genome sequence computationally.
Yeast Genome
The document summarizes the sequencing of the yeast Saccharomyces cerevisiae genome. Key points:
1) The yeast genome was sequenced between 1989-1996 by over 35 European laboratories in a collaborative effort. By 1996, the entire 12 megabase genome across 16 chromosomes had been sequenced.
2) The genome contains approximately 6,000 open reading frames that were annotated after sequencing. About 30% of yeast genes have homologs in human genes.
3) Sequencing involved creating ordered cosmid libraries, shotgun sequencing, and assembling overlapping sequences into contigs. Genes were identified and analyzed after full genome assembly.
DNA Libraries / Genomic DNA vs cDNA .pdf
This pdf is about the DNA Libraries / Genomic DNA vs cDNA.
For more details visit on YouTube; @SELF-EXPLANATORY; https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos Thanks...!
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Bio Informatics - Genome Assembly
- 1. Welcome To ❤ My ❤ Presentation
- 3. Hello! I am Marjuk Ahmed Siddiki ID: 171-15-8959 Bio-Informatics Daffodil International University
- 4. What is Genome Assembly ? 4 A genome assembly is an attempt to accurately represent an entire genome sequence from a large set of very short DNA sequences.
- 5. Genome Assembly History 5 The first genome assemblers began to appear in the late 1980s and early 1990s as variants of simpler sequence alignment programs to piece together vast quantities of fragments generated by automated sequencing instruments called DNA sequencers. As the sequenced organisms grew in size and complexity.
- 6. What is a good genome assembly ? Some of these errors can be fixed by adding more coverage and polishing the assembly. Another approach can be to use both technologies in combination and one can fairly easy produce a single contig assembly. A good assembly should be in as many pieces as the original genetic elements they represent (one contig – one chromosome) but to allow gene calling, genome alignments single base accuracy is also essential. 6
- 7. Genome Assembly Method A primer on genome assembly methods: I. Introduction II. Hierarchical III. Whole Genome Assembly IV. Hybrid Methods V. Comparative Assembly 7
- 8. Assembly Introducing The basic problem of genome assembly stems from the fact that while genomes themselves are quite large and contain long stretches of contiguous sequence, on the order of millions of base pairs), the current generation of commonly used genome sequencers can only generate relatively short segments of sequence. Traditional approaches, based on Sanger sequence could produce reads of up to 1000 bp. 8
- 9. Hierarchical The Hierarchical approach relies on mapping a set of large insert clones using methods such as Fingerprint analysis or identifying clones that contain markers localized by linkage mapping or radiation hybrid (RH).Typically, numerous clones will cover any given location of the genome. A minimal tiling path of clones 9
- 10. Whole Genome Assembly The Whole Genome Assembly (WGA) approach, which is the dominant strategy in use today, dispenses with up front mapping. The entire genome is fragmented and used to construct libraries of varying insert sizes. Typically there are libraries of some smaller size (2, 4 or 6 Kb), libraries of intermediate size (10 - 40 Kb) and libraries with large insert sequences (>100 Kb). The ends of these clones are sequenced, generating sequence reads. The reads from different ends of the same clone are referred to as mate-pairs. 10
- 11. Hybrid Approaches There is a method that combines the whole genome and hierarchical approaches. It involves supplementing limited clone mapping and low-coverage clone sequencing with whole genome sequencing. The clone- based reads are assembled first and the whole genome reads are then added to generate an 'enriched BAC (e- BAC)'. These e-BACs are then used to produce a genome assembly. 11
- 12. Comparative Assembly Another approach to assembly, which has become possible with the advent of increasing numbers of finished genomes, is comparative assembly, in which a reference genome is used to guide assembly. In this approach, rather than the overlap-layout-consensus of WGS algorithms, the assembler uses an alignment-consensus algorithm. The WGS reads are first aligned to the reference genome, which is assumed to be very similar to the newly sequenced genome.
- 13. 13
- 14. Thanks To ❤ All