The Macaque Genome: Lessons from Comparative
... about the relatedness among organisms and the traits that make them similar or different, can often be inferred by examining them at the DNA level, i.e., by looking at their DNA sequences. Comparing the DNA sequence of our own genome to other animal genomes (a field of study known as comparative gen ...
... about the relatedness among organisms and the traits that make them similar or different, can often be inferred by examining them at the DNA level, i.e., by looking at their DNA sequences. Comparing the DNA sequence of our own genome to other animal genomes (a field of study known as comparative gen ...
IGR-ANNOT: A Multiagent System for InterGenic - Inf
... computerized tools to analyze this data. • A new genome sequencing does not answer all questions about the organism. Progress is more likely to come from comparing the genomes of different organisms. ...
... computerized tools to analyze this data. • A new genome sequencing does not answer all questions about the organism. Progress is more likely to come from comparing the genomes of different organisms. ...
A whole-genome assembly of the domestic cow, Bos taurus
... Having an accurate assembly of the genome of an important species provides an invaluable substrate for future research. For example, studies of genetic diversity need a good reference genome in order to catalog differences in new strains or lineages. Expression analyses that sequence RNA from variou ...
... Having an accurate assembly of the genome of an important species provides an invaluable substrate for future research. For example, studies of genetic diversity need a good reference genome in order to catalog differences in new strains or lineages. Expression analyses that sequence RNA from variou ...
Genome Biology and
... – is a key resource for comparative genomics • to distinguish derived or ancient features of mammalian biology – mammalian innovation and adaptation • conserved non-coding sequences in particular – Provides a framework for discovering the functional ...
... – is a key resource for comparative genomics • to distinguish derived or ancient features of mammalian biology – mammalian innovation and adaptation • conserved non-coding sequences in particular – Provides a framework for discovering the functional ...
Identification of large-scale human-specific copy number
... available for this article at http://dx.doi.org/10.1007/s00439-0050130-9 and is accessible for authorized users. ...
... available for this article at http://dx.doi.org/10.1007/s00439-0050130-9 and is accessible for authorized users. ...
Genome Projector: zoomable genome map with multiple views
... biological context for the visualisation and interpretation of data, and serve as a gateway to information stored in a database [2]. For example, the popular two-dimensional genome map viewer, Gbrowse, provides an entry point for browsing the model organism genome database, GMOD [3], and biochemical ...
... biological context for the visualisation and interpretation of data, and serve as a gateway to information stored in a database [2]. For example, the popular two-dimensional genome map viewer, Gbrowse, provides an entry point for browsing the model organism genome database, GMOD [3], and biochemical ...
Tools for Comparing Bacterial Genomes
... As can be seen in > Fig. 2, the genes in this chromosome are strongly favoring one strand: the positive strand for the first (right) half and the negative strand for the second (left) half of the chromosome. These happen to be the leading strand during replication. Replication starts at the origin, ...
... As can be seen in > Fig. 2, the genes in this chromosome are strongly favoring one strand: the positive strand for the first (right) half and the negative strand for the second (left) half of the chromosome. These happen to be the leading strand during replication. Replication starts at the origin, ...
Complete Genome Sequence of Bacillus thuringiensis Strain 407 Cry-
... activities of the cry toxins, B. thuringiensis has been used widely as a biopesticide, and there is a great deal of interest to understand further its pathogenic properties and how host resistance may evolve. Strains of B. thuringiensis vary in their amenability to genetic manipulation, and acrystal ...
... activities of the cry toxins, B. thuringiensis has been used widely as a biopesticide, and there is a great deal of interest to understand further its pathogenic properties and how host resistance may evolve. Strains of B. thuringiensis vary in their amenability to genetic manipulation, and acrystal ...
Slides Here
... dedit, between A and B. • Possible edit operations: – point mutations – genome rearrangements ...
... dedit, between A and B. • Possible edit operations: – point mutations – genome rearrangements ...
ISMB2008PosterManagingGenomicData
... GMOD is a collection of interoperable open-source software components for managing, visualizing and annotating genomic data. GMOD components are used at hundreds of organizations, ranging from major model organism databases to individual labs. GMOD is well positioned to serve the converging interest ...
... GMOD is a collection of interoperable open-source software components for managing, visualizing and annotating genomic data. GMOD components are used at hundreds of organizations, ranging from major model organism databases to individual labs. GMOD is well positioned to serve the converging interest ...
Ontologies
... humans and computers annotate data in a consistent way allows data sharing across databases allows computational analysis of high-throughput “omics” datasets Objects in an ontology (eg. genes, cell types, tissue types, stages of development) are well defined. ...
... humans and computers annotate data in a consistent way allows data sharing across databases allows computational analysis of high-throughput “omics” datasets Objects in an ontology (eg. genes, cell types, tissue types, stages of development) are well defined. ...
Alternative Splicing Analysis Tools Through the UCSC Genome
... (http://www.attotron.com/cybertory/analysis/seqMassager.htm) to get rid of the numbers, white spaces and line breaks in the sequence of exon 5. You should now have the full sequence of exon 5 (in upper case), along with 14 nucleotides of the upstream intronic sequence and 6 nucleotides of the downst ...
... (http://www.attotron.com/cybertory/analysis/seqMassager.htm) to get rid of the numbers, white spaces and line breaks in the sequence of exon 5. You should now have the full sequence of exon 5 (in upper case), along with 14 nucleotides of the upstream intronic sequence and 6 nucleotides of the downst ...
bbr038online 474..484 - Oxford Academic
... conducted even by individual laboratories. However, this will yield more and more genome sequences that are not well assembled, and will hinder thorough annotation when no closely related reference genome is available. One of the challenging issues is the identification of protein-coding sequences s ...
... conducted even by individual laboratories. However, this will yield more and more genome sequences that are not well assembled, and will hinder thorough annotation when no closely related reference genome is available. One of the challenging issues is the identification of protein-coding sequences s ...
Applications of Genome Rearrangements
... Sixteen large synteny blocks are ordered differently in the X chromosomes of the human, mouse and rat. Blocks have similar gene content and order. Note that the estimated number of genes in the X chromosome is 2000. ...
... Sixteen large synteny blocks are ordered differently in the X chromosomes of the human, mouse and rat. Blocks have similar gene content and order. Note that the estimated number of genes in the X chromosome is 2000. ...
A Genome-Wide Association Study of Inbred Rat Strains
... statistically associated with variations in 42 phenotypes. This doesn't immediately seem extremely useful. Instead of focusing on the SNPs, I decided to focus on the phenotypes. What could make an organism have a bigger liver? In an attempt to discern more meaning from this list, I turned to the Rat ...
... statistically associated with variations in 42 phenotypes. This doesn't immediately seem extremely useful. Instead of focusing on the SNPs, I decided to focus on the phenotypes. What could make an organism have a bigger liver? In an attempt to discern more meaning from this list, I turned to the Rat ...
Slides, one per page - Bioinformatics and Research Computing
... program and give MACS the fragment length as an input parameter. • It uses a Poisson distribution to assign p-values to peaks. But the distribution has a dynamic parameter, local lambda, to capture the influence of local biases. • MACS default is to filter out redundant tags at the same location and ...
... program and give MACS the fragment length as an input parameter. • It uses a Poisson distribution to assign p-values to peaks. But the distribution has a dynamic parameter, local lambda, to capture the influence of local biases. • MACS default is to filter out redundant tags at the same location and ...
Document
... Step 3B: Examine VHL in UCSC Browser Enter chr3:10,177,301-10,201,372 into input box and click go. Right click on tracks NOT shown below and hide them. Right click on the RepeatMasker track and click full. It is dense by default. Adjust the zoom until you get a view you are comfortable with. ...
... Step 3B: Examine VHL in UCSC Browser Enter chr3:10,177,301-10,201,372 into input box and click go. Right click on tracks NOT shown below and hide them. Right click on the RepeatMasker track and click full. It is dense by default. Adjust the zoom until you get a view you are comfortable with. ...
pdf
... either side is 138 kb and ranges from 312 bp to 1.2 Mbp. It is a natural question whether the genes near or overlapping ultra-conserved elements tend to code for similar proteins. We divided the set of 96 genes with ultra-conserved overlap into 3 groups based on where in the gene the overlap occurre ...
... either side is 138 kb and ranges from 312 bp to 1.2 Mbp. It is a natural question whether the genes near or overlapping ultra-conserved elements tend to code for similar proteins. We divided the set of 96 genes with ultra-conserved overlap into 3 groups based on where in the gene the overlap occurre ...
Genome Databases and Open Access Resources
... • Three types of genome databases: • Databases which collect data of all sequenced genomes (Entrez_Genomes; EBI_genomes) • Databases which collect data of a category of organisms with sequenced genomes (Microbial Genomes at TIGR) • Databases specific for one organism with sequenced genomes (Flybase ...
... • Three types of genome databases: • Databases which collect data of all sequenced genomes (Entrez_Genomes; EBI_genomes) • Databases which collect data of a category of organisms with sequenced genomes (Microbial Genomes at TIGR) • Databases specific for one organism with sequenced genomes (Flybase ...
Genome
... In this exercise, we will utilize the UCSC Genome Browser to view a refined whole genome alignment of orangutan, mouse, dog, and opossum genomes to human. This alignment is produced by Multiz, a program that utilizes pairwise whole genome alignments of many species and, using a phylogenetic tree, im ...
... In this exercise, we will utilize the UCSC Genome Browser to view a refined whole genome alignment of orangutan, mouse, dog, and opossum genomes to human. This alignment is produced by Multiz, a program that utilizes pairwise whole genome alignments of many species and, using a phylogenetic tree, im ...