Genome-wide expression analysis of cultured
... Non-supervised analysis Non-supervised hierarchical clustering, using 5334 genes that were filtered on a non-parametric basis, correctly separated the trisomy 21 samples from the normal ones (Fig. 1A). Supervised analysis ANOVA was applied separately for each of the 5334 genes that were initially fi ...
... Non-supervised analysis Non-supervised hierarchical clustering, using 5334 genes that were filtered on a non-parametric basis, correctly separated the trisomy 21 samples from the normal ones (Fig. 1A). Supervised analysis ANOVA was applied separately for each of the 5334 genes that were initially fi ...
The evolution of large DNA viruses: combining genomic information
... only known viral homologue, the bovine herpesvirus 4 Bo17 protein [23]. A phylogenetic analysis revealed that the gene was captured by the virus after the split between African buffalo and cattle at w1.5 million years ago. Since that time the viral gene, which is thought to reduce the ability of imm ...
... only known viral homologue, the bovine herpesvirus 4 Bo17 protein [23]. A phylogenetic analysis revealed that the gene was captured by the virus after the split between African buffalo and cattle at w1.5 million years ago. Since that time the viral gene, which is thought to reduce the ability of imm ...
Genes Identified by Visible Mutant Phenotypes Show Increased Bias
... subgenome is significantly greater than for the classical maize gene list as a whole (p = .028, Fisher Exact Test), and members of homeologous gene pairs located on maize1 were twice as likely as the duplicate copies on maize2 to be originally identified by mutant phenotype -- 29 maize1 genes with h ...
... subgenome is significantly greater than for the classical maize gene list as a whole (p = .028, Fisher Exact Test), and members of homeologous gene pairs located on maize1 were twice as likely as the duplicate copies on maize2 to be originally identified by mutant phenotype -- 29 maize1 genes with h ...
CGH Microarray Solutions for Genome-Wide Genetic Analysis
... Agilent’s 2-color CGH array provides superior copy number data as opposed to 1-color because sample and reference DNA are directly compared. Agilent’s long 60-mer probes are more specific than probes that are shorter in length, allowing you to use fewer probes to make accurate calls. ...
... Agilent’s 2-color CGH array provides superior copy number data as opposed to 1-color because sample and reference DNA are directly compared. Agilent’s long 60-mer probes are more specific than probes that are shorter in length, allowing you to use fewer probes to make accurate calls. ...
Integrons and the Origin of Antibiotic Resistance Gene Cassettes
... repeats), led to discovery of another type of integron, a superintegron (SI) (Fig. 2). This distinct type of integron is now known to be an integral component of many g-proteobacterial genomes. The integron discovered in chromosome 2 of V. cholerae possesses a specific integrase, IntIA, that is rela ...
... repeats), led to discovery of another type of integron, a superintegron (SI) (Fig. 2). This distinct type of integron is now known to be an integral component of many g-proteobacterial genomes. The integron discovered in chromosome 2 of V. cholerae possesses a specific integrase, IntIA, that is rela ...
DpnII - Inv. PCR of miniMos for distribution
... protocol because we changed and optimized several parameters which in our hands improve the reliability of inverse PCR reactions. It is the protocol that we currently (December 2012) use in the lab. Use aerosol resistant tips for all steps!! Contamination is a real problem when doing two sequential ...
... protocol because we changed and optimized several parameters which in our hands improve the reliability of inverse PCR reactions. It is the protocol that we currently (December 2012) use in the lab. Use aerosol resistant tips for all steps!! Contamination is a real problem when doing two sequential ...
Structural organization of the malaria mosquito heterochromatin
... performed using antibodies against Heterochromatin Protein 1 (HP1) and lamin Dm0 Drosophila melanogaster. Physical mapping was done by Cy3, Cy5 labeled PCR amplified genes. The bioinformatics analysis was conducted using C program ATCONTENT, Biomart and SMARTest. We developed novel Bayesian statisti ...
... performed using antibodies against Heterochromatin Protein 1 (HP1) and lamin Dm0 Drosophila melanogaster. Physical mapping was done by Cy3, Cy5 labeled PCR amplified genes. The bioinformatics analysis was conducted using C program ATCONTENT, Biomart and SMARTest. We developed novel Bayesian statisti ...
Protein Sequence Alignment and Database Searching
... Alignment of Multiple Sequences Extending Dynamic Programming to more sequences –Dynamic programming can be extended for more than two –In practice it requires CPU and Memory (Murata et al 1985) – MSA, Limited only up to 8-10 sequences (1989) –DCA (Divide and Conquer; Stoye et al., 1997), 20-25 seq ...
... Alignment of Multiple Sequences Extending Dynamic Programming to more sequences –Dynamic programming can be extended for more than two –In practice it requires CPU and Memory (Murata et al 1985) – MSA, Limited only up to 8-10 sequences (1989) –DCA (Divide and Conquer; Stoye et al., 1997), 20-25 seq ...
Construction of nanA mutants
... Construction of nanA mutants This was carried out by the Janus cassette mutagenesis essentially as described by Sung, et al, 2001 (Appl. Environ. Microbiol., Nov. 2001, p. 5190–5196) , as follows. Construction of in-frame, insertion of the Janus cassette (KanR rpsL) in replacement of the nanA gene. ...
... Construction of nanA mutants This was carried out by the Janus cassette mutagenesis essentially as described by Sung, et al, 2001 (Appl. Environ. Microbiol., Nov. 2001, p. 5190–5196) , as follows. Construction of in-frame, insertion of the Janus cassette (KanR rpsL) in replacement of the nanA gene. ...
Functional gene groups are concentrated within chromosomes
... of a different nature: The two members of a PPI are in direct physical contact under some conditions, while complex members are simultaneously involved as building blocks in the same physical unit. In contrast, pathways summarize sequences of multiple chemical or signaling reactions, and hence some ...
... of a different nature: The two members of a PPI are in direct physical contact under some conditions, while complex members are simultaneously involved as building blocks in the same physical unit. In contrast, pathways summarize sequences of multiple chemical or signaling reactions, and hence some ...
Genetics and Biotechnology
... from India that have a high heat tolerance but produce poor beef. The new breed, Santa Gertrudis, produces excellent beef and can live in hot environments. Which ...
... from India that have a high heat tolerance but produce poor beef. The new breed, Santa Gertrudis, produces excellent beef and can live in hot environments. Which ...
source file - MIMG — UCLA
... Record the DNA coordinates for this ORF either your lab notebook as part of first module. Provide a from the sequence viewer. It is also available in comment in current module indicating the original your lab notebook from the first module. coordinates are likely correct. ...
... Record the DNA coordinates for this ORF either your lab notebook as part of first module. Provide a from the sequence viewer. It is also available in comment in current module indicating the original your lab notebook from the first module. coordinates are likely correct. ...
Where Do New Genes Come From? A Computational Analysis of
... • Therefore, for all k, there will always be a cluster of size at least k • Therefore, the probability of finding a cluster of size at least k is always one! ...
... • Therefore, for all k, there will always be a cluster of size at least k • Therefore, the probability of finding a cluster of size at least k is always one! ...
MAK, a computational tool kit for automated MITE
... retrieved. The results for all the significant hits can be exported as a table. Implementation of MAK MAK runs on UNIX, Linux and Win32 platforms on which Perl 5.6.1 (http://www.perl.com) and Bioperl 1.0.2 releases (http://www.bioperl.org) are installed. The web-based software (http://perl.idmb.tamu ...
... retrieved. The results for all the significant hits can be exported as a table. Implementation of MAK MAK runs on UNIX, Linux and Win32 platforms on which Perl 5.6.1 (http://www.perl.com) and Bioperl 1.0.2 releases (http://www.bioperl.org) are installed. The web-based software (http://perl.idmb.tamu ...
Week4-Blast/MSA
... Smith-Waterman algorithm (JMB 147:195-97, 1981) • A set of heuristics were applied to the above algorithm to make it less greedy, so it is less sensitive but runs faster • Implements Dynamic programming • Provide local alignment between two sequences • Both BLAST and FASTA use this algorithm wit ...
... Smith-Waterman algorithm (JMB 147:195-97, 1981) • A set of heuristics were applied to the above algorithm to make it less greedy, so it is less sensitive but runs faster • Implements Dynamic programming • Provide local alignment between two sequences • Both BLAST and FASTA use this algorithm wit ...
Cellecta Technical Note - RNAi Screen - PUMA
... they are missing from the library. Thus, although the library was constructed with 200,000 shRNAs, it seems that approximately 40% of the shRNA are missing. This indicates that there is probably also a large variability in the remaining sequences with some being very abundant and others in low numbe ...
... they are missing from the library. Thus, although the library was constructed with 200,000 shRNAs, it seems that approximately 40% of the shRNA are missing. This indicates that there is probably also a large variability in the remaining sequences with some being very abundant and others in low numbe ...
Genome
... In this exercise, we will use BLAST (Basic Local Alignment Search Tool) to search for significant occurrences of a class of transposable elements (TEs) called Short INterspersed Elements (SINEs), specifically of the ALU family, in the well-known VHL tumor suppressor gene. The goal of this exercise i ...
... In this exercise, we will use BLAST (Basic Local Alignment Search Tool) to search for significant occurrences of a class of transposable elements (TEs) called Short INterspersed Elements (SINEs), specifically of the ALU family, in the well-known VHL tumor suppressor gene. The goal of this exercise i ...
Analysis of Drosophila Species Genome Size and Satellite DNA
... Accepted for publication June 20, 2007 ABSTRACT The size of eukaryotic genomes can vary by several orders of magnitude, yet genome size does not correlate with the number of genes nor with the size or complexity of the organism. Although ‘‘whole’’-genome sequences, such as those now available for 12 ...
... Accepted for publication June 20, 2007 ABSTRACT The size of eukaryotic genomes can vary by several orders of magnitude, yet genome size does not correlate with the number of genes nor with the size or complexity of the organism. Although ‘‘whole’’-genome sequences, such as those now available for 12 ...
Estimates of DNA and Protein Sequence Divergence: An
... These initial conditions are the expected values for a random choice of one sequence for each of the two populations from the original population. Since the speciation process may involve substantial sampling error (Templeton 1980), the initial values of
... These initial conditions are the expected values for a random choice of one sequence for each of the two populations from the original population. Since the speciation process may involve substantial sampling error (Templeton 1980), the initial values of
abstracts
... between the maps of seven different Prunus species (almond, peach, apricot, cherry, P. ferganensis, P. davidiana and P. cerasifera) that were found to be essentially collinear. Comparisons with apple, still at its beginning, indicate a high level of synteny. A much more fragmentary pattern of synten ...
... between the maps of seven different Prunus species (almond, peach, apricot, cherry, P. ferganensis, P. davidiana and P. cerasifera) that were found to be essentially collinear. Comparisons with apple, still at its beginning, indicate a high level of synteny. A much more fragmentary pattern of synten ...
Rampant horizontal gene transfer and phospho
... well-supported clade. Within group B1, we found both the monophyly of Thermus + Deinococcus and that of Cytophaga + Bacteroides. Yet, other regions of the tree are more puzzling. Some species that are thought to be closely related are separated among several groups (e.g., the alpha-proteobacteria in ...
... well-supported clade. Within group B1, we found both the monophyly of Thermus + Deinococcus and that of Cytophaga + Bacteroides. Yet, other regions of the tree are more puzzling. Some species that are thought to be closely related are separated among several groups (e.g., the alpha-proteobacteria in ...
Phytochemical Analysis and In-Vitro
... Plants and herbal medicines have important position in modern medicine, due to their chemical and medicinal contents found in natural form. They contain various secondary metabolites which work together and show wide range of antibacterial activities. Microorganisms may get mutated and become resist ...
... Plants and herbal medicines have important position in modern medicine, due to their chemical and medicinal contents found in natural form. They contain various secondary metabolites which work together and show wide range of antibacterial activities. Microorganisms may get mutated and become resist ...
Full text in pdf - International Microbiology
... Rapid spectrofluorometric screening of poly-hydroxyalkanoate-producing bacteria from microbial mats ...
... Rapid spectrofluorometric screening of poly-hydroxyalkanoate-producing bacteria from microbial mats ...
Expansion of the Pseudo-autosomal Region and Ongoing
... than has previously been available and will also be useful for other investigations using this species (Bernasconi et al. 2009). Although whole-genome sequencing can identify many genes and locate them on chromosomes, it is impractical for S. latifolia, due to its large genome size of almost 3 Gb (C ...
... than has previously been available and will also be useful for other investigations using this species (Bernasconi et al. 2009). Although whole-genome sequencing can identify many genes and locate them on chromosomes, it is impractical for S. latifolia, due to its large genome size of almost 3 Gb (C ...
Lecture II: Genomic Methods
... Genotyping - Limitations & quality control • Accuracy of algorithm – Depends on number of samples in each cluster – Prone to errors for small number of samples or SNP’s with rare alleles ...
... Genotyping - Limitations & quality control • Accuracy of algorithm – Depends on number of samples in each cluster – Prone to errors for small number of samples or SNP’s with rare alleles ...
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.