The complete mitochondrial genome of the demosponge
... programs were kept for the phylogenetic analyses. Additionally, positions in which gaps are present in more than 25% of the taxa were manually removed. The protein-coding gene data set included 3619 characters, 1386 of which were parsimony informative and 1356 invariant. The concatenated alignment o ...
... programs were kept for the phylogenetic analyses. Additionally, positions in which gaps are present in more than 25% of the taxa were manually removed. The protein-coding gene data set included 3619 characters, 1386 of which were parsimony informative and 1356 invariant. The concatenated alignment o ...
In recent times the incidence of multiple drug resistant pathogens
... This paper looks at the mechanisms for horizontal gene transfer, and the implications of using antibiotic resistance marker genes in Genetically Modified Plants and their derived products. This examination is done in the context of the controversial genetically modified maize variety Bt10 which was ...
... This paper looks at the mechanisms for horizontal gene transfer, and the implications of using antibiotic resistance marker genes in Genetically Modified Plants and their derived products. This examination is done in the context of the controversial genetically modified maize variety Bt10 which was ...
Slide 1
... RAPD markers need to be converted to stable PCR markers The polymorphic RAPD marker band is isolated from the gel It is used a template and re-PCRed The new PCR product is cloned and sequenced Once the sequence is determined, new longer and specific primers can be designed ...
... RAPD markers need to be converted to stable PCR markers The polymorphic RAPD marker band is isolated from the gel It is used a template and re-PCRed The new PCR product is cloned and sequenced Once the sequence is determined, new longer and specific primers can be designed ...
Developing codominant PCR markers in pines
... Forest trees are different from nearly all other crop plants in that even the most commercially important species are relatively undomesticated. As was pointed out some time ago (Libby et al. 1969) this feature brings both opportunities and responsibilities. While we are very much interested in bree ...
... Forest trees are different from nearly all other crop plants in that even the most commercially important species are relatively undomesticated. As was pointed out some time ago (Libby et al. 1969) this feature brings both opportunities and responsibilities. While we are very much interested in bree ...
b. genetic engineering.
... DNA is separated from the other cell parts. • B. Cutting DNA- cut into small fragment by restriction enzymes (cut DNA at a specific sequence of nucleotides). • C. Separating DNA – method is gel ...
... DNA is separated from the other cell parts. • B. Cutting DNA- cut into small fragment by restriction enzymes (cut DNA at a specific sequence of nucleotides). • C. Separating DNA – method is gel ...
Weldon_McVean - Wellcome Trust Centre for Human Genetics
... At least two shared SNPs in 4kb with the same LD ...
... At least two shared SNPs in 4kb with the same LD ...
What is SNP?
... accelerate our understanding of the molecular basis of cancer through the application of genome analysis technologies, including large-scale sequencing ...
... accelerate our understanding of the molecular basis of cancer through the application of genome analysis technologies, including large-scale sequencing ...
Identification of bacterial agent(s) for acute hepatopancreatic
... bacterial infections (www.enaca.org). However, the potential cause(s) of the disease is still under ...
... bacterial infections (www.enaca.org). However, the potential cause(s) of the disease is still under ...
- Wiley Online Library
... With full genome sequencing of bacterial genomes becoming more affordable, the number of publications, which deploy this elegant and modern technique is rapidly increasing. Full genome sequences of hundreds of bacterial strains have been determined and described. However, on reading some of the lite ...
... With full genome sequencing of bacterial genomes becoming more affordable, the number of publications, which deploy this elegant and modern technique is rapidly increasing. Full genome sequences of hundreds of bacterial strains have been determined and described. However, on reading some of the lite ...
Nature template
... Table 3 – Multiple regression coefficients for the relationship between potential nitrification and environmental variables (salinity, DO, sediment chlorophyll a,) and abundance of AOA amoA genes. Standardized coefficients and levels of significance (p values) are listed. ...
... Table 3 – Multiple regression coefficients for the relationship between potential nitrification and environmental variables (salinity, DO, sediment chlorophyll a,) and abundance of AOA amoA genes. Standardized coefficients and levels of significance (p values) are listed. ...
1 - BioMed Central
... TM is the annealing temperature as listed in Table S1. Steps 2 to 4 were repeated 33 times in sequence. PMut In some cases, the program did not have sufficient confidence in the results due to the high protein sequence divergence between chicken and other well-studied species with which it was compa ...
... TM is the annealing temperature as listed in Table S1. Steps 2 to 4 were repeated 33 times in sequence. PMut In some cases, the program did not have sufficient confidence in the results due to the high protein sequence divergence between chicken and other well-studied species with which it was compa ...
chromosomes - HCC Learning Web
... - LINEs (long interspersed repeated sequences) with sequences of 1,000–7,000 bp or more. The common example in mammals is LINE-1, with sequences up to 7 kb in length, that can act as transposons - SINEs (short interspersed repeated sequences) with sequences of 100–500 bp. An example is the Alu repea ...
... - LINEs (long interspersed repeated sequences) with sequences of 1,000–7,000 bp or more. The common example in mammals is LINE-1, with sequences up to 7 kb in length, that can act as transposons - SINEs (short interspersed repeated sequences) with sequences of 100–500 bp. An example is the Alu repea ...
Hierarchical clustering
... (i) “MEAN-LOG-P” statistic which is calculated as mean(log(p-value)) (ii) Thresholded mean statistic (“LoMean”), which is calculated by settting all p-values above t equal to t (with, e.g., t=0.25) and taking the arithmetic mean of the resulting values; (iii) LoMLP which is a hybrid of the “LoMean” ...
... (i) “MEAN-LOG-P” statistic which is calculated as mean(log(p-value)) (ii) Thresholded mean statistic (“LoMean”), which is calculated by settting all p-values above t equal to t (with, e.g., t=0.25) and taking the arithmetic mean of the resulting values; (iii) LoMLP which is a hybrid of the “LoMean” ...
Molecular Cell Biology - Biomedical Informatics
... (http://www.dbtss.hgc.jp/index.html) were used for statistical analyses as two separate datasets. We also constructed a small test set of 27 human promoters with MSS. This set was utilized to analyze the statistics of core-promoter elements in MSS promoters. Each promoter was considered several time ...
... (http://www.dbtss.hgc.jp/index.html) were used for statistical analyses as two separate datasets. We also constructed a small test set of 27 human promoters with MSS. This set was utilized to analyze the statistics of core-promoter elements in MSS promoters. Each promoter was considered several time ...
Identifying a Novel Isoform of the AZIN1 Gene by Combining High
... by combining high-throughput and traditional sequencing methods to find and validate a novel isoform of the AZIN1 gene in peripheral blood mononuclear cells (PBMCs). The procedure included the following steps: (1) separation of PBMCs from whole blood (2) extraction of RNA from PBMCs (3) creation of ...
... by combining high-throughput and traditional sequencing methods to find and validate a novel isoform of the AZIN1 gene in peripheral blood mononuclear cells (PBMCs). The procedure included the following steps: (1) separation of PBMCs from whole blood (2) extraction of RNA from PBMCs (3) creation of ...
Ch. 5: Presentation Slides
... DNA Sequence: convention 5’ to 3’end, one strand (because other strand is complementary and therefore known also) ...
... DNA Sequence: convention 5’ to 3’end, one strand (because other strand is complementary and therefore known also) ...
here - Statistics for Innovation (sfi)
... FWER: Alternatives to Bonferroni • There are alternative methods for FWER p-value adjustment. • The Westfall-Young method (based on permutations of the sample labels) takes the correlation between genes into account and is typically more powerful for microarray data. • See the Bioconductor package ...
... FWER: Alternatives to Bonferroni • There are alternative methods for FWER p-value adjustment. • The Westfall-Young method (based on permutations of the sample labels) takes the correlation between genes into account and is typically more powerful for microarray data. • See the Bioconductor package ...
Supplementary material for "The Plasmodium HU homolog, which
... 1.4. Transfection of parasite and localization of expressed fluorescent proteins The bsd gene of the plasmids pEM7/Bsd (Invitrogen) was recombined to the P. falciparum expression plasmids pSSPF2/PfHsp60-GFP [1] and pSSPF2/PfACP-DsRed [3] replacing the hDHFR gene to generate pSSPF3/PfHsp60-GFP and pS ...
... 1.4. Transfection of parasite and localization of expressed fluorescent proteins The bsd gene of the plasmids pEM7/Bsd (Invitrogen) was recombined to the P. falciparum expression plasmids pSSPF2/PfHsp60-GFP [1] and pSSPF2/PfACP-DsRed [3] replacing the hDHFR gene to generate pSSPF3/PfHsp60-GFP and pS ...
Intraspecies variation in bacterial genomes: the need for a
... variation. after digestion of chromosomal DNA by rare-cutting enzymes, has greatly advanced our understanding of Assessing genome variation within species species genome structure. Macrorestriction mapping It has long been known that bacteria can carry plas- detects genome rearrangements as well as ...
... variation. after digestion of chromosomal DNA by rare-cutting enzymes, has greatly advanced our understanding of Assessing genome variation within species species genome structure. Macrorestriction mapping It has long been known that bacteria can carry plas- detects genome rearrangements as well as ...
Human genome project : Pharmacogenomics and drug development
... their estimation only about 0.5-1% of the genome has been targeted by therapeutics. Obviously not all genes will encode viable therapeutic targets but it is likely that a significant number of genes will, and they remam undiscovered or, as yet undiscovered. Genomics actiVlttes such as high throughpu ...
... their estimation only about 0.5-1% of the genome has been targeted by therapeutics. Obviously not all genes will encode viable therapeutic targets but it is likely that a significant number of genes will, and they remam undiscovered or, as yet undiscovered. Genomics actiVlttes such as high throughpu ...
Gene Prediction Techniques - Computational Biology of RNA
... The finding of protein-coding genes on a genome sequence is a complex task. Within millions of non-coding nucleotides, very short stretches of DNA which actually code for a protein (coding exons) lie scattered. This tiny coding fraction, can be unveiled making use of the biological properties and th ...
... The finding of protein-coding genes on a genome sequence is a complex task. Within millions of non-coding nucleotides, very short stretches of DNA which actually code for a protein (coding exons) lie scattered. This tiny coding fraction, can be unveiled making use of the biological properties and th ...
Identification of Prokaryotic Small Proteins using a Comparative
... databases. Further complicating the problem is a contamination of sequence databases caused by the propagation of dubious ORF predictions via homology-based annotation efforts [9]. In situations where there is no matching protein, sequence-composition-based methods are traditionally used. There are ...
... databases. Further complicating the problem is a contamination of sequence databases caused by the propagation of dubious ORF predictions via homology-based annotation efforts [9]. In situations where there is no matching protein, sequence-composition-based methods are traditionally used. There are ...
Supplementary Material for: A scaling normalization method for
... differential expression). In all plots, the black points represent the estimates with the unweighted trimmed mean (trim=.45), weighted trimmed mean (logratiotrim=.25, Avaluetrim=.05) and a robust linear model with MM estimation. The top left panel plots the estimated factors versus the true factors; ...
... differential expression). In all plots, the black points represent the estimates with the unweighted trimmed mean (trim=.45), weighted trimmed mean (logratiotrim=.25, Avaluetrim=.05) and a robust linear model with MM estimation. The top left panel plots the estimated factors versus the true factors; ...
Evaluation of Potential HIV Candidate Vaccines
... • The ABI PRISM® 7900HT: real-time PCR system that detects & quantitates nucleic acid sequences. Automation & 384-well plate capability allow for very high-throughput. • Interchangeable formats (96 & 384 well) provide flexibility • Hand-held and integrated bar code readers simplify sample tracking • ...
... • The ABI PRISM® 7900HT: real-time PCR system that detects & quantitates nucleic acid sequences. Automation & 384-well plate capability allow for very high-throughput. • Interchangeable formats (96 & 384 well) provide flexibility • Hand-held and integrated bar code readers simplify sample tracking • ...
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.