Case Study: Visualization of annotated DNA sequences
... semantic zooming and annotation comparison, but zooming and panning is not real-time (VIII) and the browser does not support DNA sequence comparisons (X). Therefore, we have developed a DNA visualization tool that fulfills all defined requirements. DNAVis is written in C++ and runs on both Windows a ...
... semantic zooming and annotation comparison, but zooming and panning is not real-time (VIII) and the browser does not support DNA sequence comparisons (X). Therefore, we have developed a DNA visualization tool that fulfills all defined requirements. DNAVis is written in C++ and runs on both Windows a ...
Four types of evolution
... that species could not have been created in their present form, in their present locations, it was clear that species could not have been created. That implicitly left only Darwin‟s theory. It was Hobson‟s choice – the theory of common descent or nothing. We need to be sure, then, that this really i ...
... that species could not have been created in their present form, in their present locations, it was clear that species could not have been created. That implicitly left only Darwin‟s theory. It was Hobson‟s choice – the theory of common descent or nothing. We need to be sure, then, that this really i ...
R and BioConductor
... • Global Lowess/Loess: l = the expected value after locally fitting a smooth regression curve on the global MA plot. • Print-tip Lowess/Loess: l = the loess/lowess fit to the MA-plot for different print-tips. ...
... • Global Lowess/Loess: l = the expected value after locally fitting a smooth regression curve on the global MA plot. • Print-tip Lowess/Loess: l = the loess/lowess fit to the MA-plot for different print-tips. ...
Genome Annotation
... stop codon) and for the other 2 forward, incorrect reading frames. If the correct frame score exceeds the incorrect frame scores by a certain amount, this ORF is accepted as protein-coding. After a good ORF is found, it is extended 5’ to find possible start codons (but only allowing 6 bases of overl ...
... stop codon) and for the other 2 forward, incorrect reading frames. If the correct frame score exceeds the incorrect frame scores by a certain amount, this ORF is accepted as protein-coding. After a good ORF is found, it is extended 5’ to find possible start codons (but only allowing 6 bases of overl ...
Changes in DNA
... DNA but not the protein. Therefore they are called neutral mutations, mutations which should have no effect on the organism’s phenotype. 2. Missense mutations. Missense mutations substitute one amino acid for another. Some missense mutations have very large effects, while others have minimal or no e ...
... DNA but not the protein. Therefore they are called neutral mutations, mutations which should have no effect on the organism’s phenotype. 2. Missense mutations. Missense mutations substitute one amino acid for another. Some missense mutations have very large effects, while others have minimal or no e ...
Elucidating the essentiality of essential genes in E. coli K-12
... essential genes in LB medium [2]. Elucidating the essentiality of these essential genes is a key to understand the system level organization of living cells. Here we present our analysis to address this issue from the perspectives of protein-protein interaction and metabolic networks. We have perfor ...
... essential genes in LB medium [2]. Elucidating the essentiality of these essential genes is a key to understand the system level organization of living cells. Here we present our analysis to address this issue from the perspectives of protein-protein interaction and metabolic networks. We have perfor ...
Chapter-4-Lecture
... of key genes during brain development that increases a boy’s attraction to his own sex. The explanation obviously does not hold true for all cases of homosexuality, but it may provide important clues into the origin of heterosexual as well as homosexual orientation for some people. ...
... of key genes during brain development that increases a boy’s attraction to his own sex. The explanation obviously does not hold true for all cases of homosexuality, but it may provide important clues into the origin of heterosexual as well as homosexual orientation for some people. ...
Gene Name
... silenced at the same times during ES cell differentiation (ie. are present in the same cluster), we took all the genes that had been assigned to a cluster and for which positional information was available (118, Mouse Genome Informatics (MGI) www.informatics.jax.org) and listed the possible gene pai ...
... silenced at the same times during ES cell differentiation (ie. are present in the same cluster), we took all the genes that had been assigned to a cluster and for which positional information was available (118, Mouse Genome Informatics (MGI) www.informatics.jax.org) and listed the possible gene pai ...
Introduction to self-assembly Self
... both natural and synthetic biological systems, in many cases assembly requires a more direct agent. If that agent is an already-assembled entity of the same type, the process is still considered a form of self-assembly but is more likely to be referred to as self-replication. The “RNA world” hypoth ...
... both natural and synthetic biological systems, in many cases assembly requires a more direct agent. If that agent is an already-assembled entity of the same type, the process is still considered a form of self-assembly but is more likely to be referred to as self-replication. The “RNA world” hypoth ...
this poster
... suppress the proliferation of transposons in plants and animals. In plants such processes for transposon silencing have been suggested to act in both the female and male gametophytes. Argonaute proteins are key players in RNA dependent silencing mechanism and we are interested in investigating the r ...
... suppress the proliferation of transposons in plants and animals. In plants such processes for transposon silencing have been suggested to act in both the female and male gametophytes. Argonaute proteins are key players in RNA dependent silencing mechanism and we are interested in investigating the r ...
Biotechnology
... a) determine the difference in base _________ between a normal gene and a mutated gene b) use the genes to genetically _______ organisms in a beneficial way When cloned genes are used to modify a human, the process is called ______________ Otherwise, organisms are called ___________ organisms (trans ...
... a) determine the difference in base _________ between a normal gene and a mutated gene b) use the genes to genetically _______ organisms in a beneficial way When cloned genes are used to modify a human, the process is called ______________ Otherwise, organisms are called ___________ organisms (trans ...
Illumina Infinium HumanMethylation450 BeadChip Data
... powerful embedded statistics and visualizations to yield deep biological interpretation. Going from raw data to biological interpretation has never been easier. ...
... powerful embedded statistics and visualizations to yield deep biological interpretation. Going from raw data to biological interpretation has never been easier. ...
Recombination and Genetic Engineering
... Class l or "compound Tns" encode drug resistance genes flanked by copies of an IS in a direct or indirect repeat. A direct repeat exists when the two sequences at either end are oriented in the same direction while an indirect (or inverted) repeat exists when they are in opposite directions. In this ...
... Class l or "compound Tns" encode drug resistance genes flanked by copies of an IS in a direct or indirect repeat. A direct repeat exists when the two sequences at either end are oriented in the same direction while an indirect (or inverted) repeat exists when they are in opposite directions. In this ...
Supplementary information - Springer Static Content Server
... laboratory strains have been sequenced, and it has been observed that there is significant variation between strains 1. Two major sources of laboratory strains have been investigated, MG1655, by Fred Blattner and co-workers 2, and W3110 by Hirotada Mori and co-workers (origin of the Keio collection ...
... laboratory strains have been sequenced, and it has been observed that there is significant variation between strains 1. Two major sources of laboratory strains have been investigated, MG1655, by Fred Blattner and co-workers 2, and W3110 by Hirotada Mori and co-workers (origin of the Keio collection ...
Tasmanian Devil gene annotation methods
... Targeted Stage: Generating coding models from devil evidence Devil protein sequences were downloaded from public databases (UniProt SwissProt/TrEMBL [8] and Genbank) and filtered to remove sequences based on predictions. The devil sequences were mapped to the genome using Pmatch as indicated in Figu ...
... Targeted Stage: Generating coding models from devil evidence Devil protein sequences were downloaded from public databases (UniProt SwissProt/TrEMBL [8] and Genbank) and filtered to remove sequences based on predictions. The devil sequences were mapped to the genome using Pmatch as indicated in Figu ...
polymerase chain reaction
... vitro; insert the cloned, desired gene into the nuclei of the eggs; some eggs will integrate the injected DNA into the genomic DNA; gene product is expressed; these eggs are them implanted into mother; embryo develops and it has the “new” genes. ...
... vitro; insert the cloned, desired gene into the nuclei of the eggs; some eggs will integrate the injected DNA into the genomic DNA; gene product is expressed; these eggs are them implanted into mother; embryo develops and it has the “new” genes. ...
How are living things organized?
... How are living things organized? Diversity and Classification ...
... How are living things organized? Diversity and Classification ...
Supplementary materials
... and Average-linkage uses the mean of all genes in the group. Statistical studies have shown that Single-linkage clusters are often worse than random associations while Complete-linkage consistently generates a stable cluster (Yeung et al., 2001; Gibbons and Roth, 2002). Genes belonging to common sub ...
... and Average-linkage uses the mean of all genes in the group. Statistical studies have shown that Single-linkage clusters are often worse than random associations while Complete-linkage consistently generates a stable cluster (Yeung et al., 2001; Gibbons and Roth, 2002). Genes belonging to common sub ...
Alignment of pairs of sequences
... Why compare sequences? • To find whether two (or more) genes or proteins are evolutionarily related to each other • To find structurally or functionally similar regions within proteins ...
... Why compare sequences? • To find whether two (or more) genes or proteins are evolutionarily related to each other • To find structurally or functionally similar regions within proteins ...
Genetic Engineering
... Problems with PCR • Contamination: Need a clean room environment. No dust mites or bacteria • Small segments of DNA: if its too big the primer will attach to the wrong thing, an incorrect DNA sequence would result. • The nucleotide sequence must be known in order to create the correct primers. • Di ...
... Problems with PCR • Contamination: Need a clean room environment. No dust mites or bacteria • Small segments of DNA: if its too big the primer will attach to the wrong thing, an incorrect DNA sequence would result. • The nucleotide sequence must be known in order to create the correct primers. • Di ...
Florida Department of Law Enforcement`s Convicted Offender DNA
... hopefully give the unit the capability to handle the STR analysis of the 51,000 samples already collected. In addition to the current database, we hope to make legislative changes to increase the number of offenses requiring collection with the ultimate goal of collecting all the convicted felons wi ...
... hopefully give the unit the capability to handle the STR analysis of the 51,000 samples already collected. In addition to the current database, we hope to make legislative changes to increase the number of offenses requiring collection with the ultimate goal of collecting all the convicted felons wi ...
paper by Acquisti, Elser and Kumar
... goldenPath/currentGenomes/) for D. melanogaster (Release 5, FlyBase Gene Models), and for H. sapiens (hg18, RefSeq Gene Models). In a previous analysis of many complete animal genomes (Elser et al. 2006), these genomes were found to be typical animal representatives, with the exception of species in ...
... goldenPath/currentGenomes/) for D. melanogaster (Release 5, FlyBase Gene Models), and for H. sapiens (hg18, RefSeq Gene Models). In a previous analysis of many complete animal genomes (Elser et al. 2006), these genomes were found to be typical animal representatives, with the exception of species in ...
Engineering of E.coli for production of poly(3
... the microbial P3HP production from glycerol was improved greatly by constructing a genetically stable E.coli recombinant strain To overcome the instability due to plasmid loss, two strategies were tested and combined ...
... the microbial P3HP production from glycerol was improved greatly by constructing a genetically stable E.coli recombinant strain To overcome the instability due to plasmid loss, two strategies were tested and combined ...
Metagenomics
Metagenomics is the study of genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. While traditional microbiology and microbial genome sequencing and genomics rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods. Recent studies use either ""shotgun"" or PCR directed sequencing to get largely unbiased samples of all genes from all the members of the sampled communities. Because of its ability to reveal the previously hidden diversity of microscopic life, metagenomics offers a powerful lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world. As the price of DNA sequencing continues to fall, metagenomics now allows microbial ecology to be investigated at a much greater scale and detail than before.