File formats for NGS data - Bioinformatics Training Materials
... ● Allows for genes and genomic features to be evaluated in their genomic context. ○ Gene A is close to gene B ○ Gene A and gene B are within feature C ● Can be used to align shallow targeted high-throughput sequencing to a pre-built map of an organism ...
... ● Allows for genes and genomic features to be evaluated in their genomic context. ○ Gene A is close to gene B ○ Gene A and gene B are within feature C ● Can be used to align shallow targeted high-throughput sequencing to a pre-built map of an organism ...
Databases - Orly Alter`s
... http://www.alterlab.org/teaching/BIOEN6770/labs/Spellman_Cell_Cycle.txt – download the Spellman et al. alpha-factor block-release data as follows: a) Gene Selection and Annotation: Enter the list of YORFs alphabetically sorted. Use experiment name. Include “Biological Process,” “Cellular Component,” ...
... http://www.alterlab.org/teaching/BIOEN6770/labs/Spellman_Cell_Cycle.txt – download the Spellman et al. alpha-factor block-release data as follows: a) Gene Selection and Annotation: Enter the list of YORFs alphabetically sorted. Use experiment name. Include “Biological Process,” “Cellular Component,” ...
Katsarou Dimitra
... CDSs of glucosinolate biosynthesis and regulatory genes obtained from NCBI database were used to design specific and degenerated primers in order to amplify one part of the sequence of each gene we were interesting in. Primers were designed based on conserved areas of genes of other Brassicaceae pla ...
... CDSs of glucosinolate biosynthesis and regulatory genes obtained from NCBI database were used to design specific and degenerated primers in order to amplify one part of the sequence of each gene we were interesting in. Primers were designed based on conserved areas of genes of other Brassicaceae pla ...
Legends
... were obtained by total RNA extraction followed by Illumina sequencing. RPKM values were determined by mapping the reads against the human genome using GEM and then “pairing” the reads onto the annotated transcripts from the RefSeq databank using Flux Capacitor. ctl_cyt_expr_up ctl_cyt_expr_down List ...
... were obtained by total RNA extraction followed by Illumina sequencing. RPKM values were determined by mapping the reads against the human genome using GEM and then “pairing” the reads onto the annotated transcripts from the RefSeq databank using Flux Capacitor. ctl_cyt_expr_up ctl_cyt_expr_down List ...
ppt for
... per cycle to image the entire channel area. The surface area needed to accommodate ~350,000 mRNA molecules contained in a single cell is ~0.4 mm2; thus, only eight images per cycle would be needed. Sequence analysis can be done with direct RNA sequencing (DRS) or on-surface cDNA synthesis followed b ...
... per cycle to image the entire channel area. The surface area needed to accommodate ~350,000 mRNA molecules contained in a single cell is ~0.4 mm2; thus, only eight images per cycle would be needed. Sequence analysis can be done with direct RNA sequencing (DRS) or on-surface cDNA synthesis followed b ...
Lecture 15 Biol302 Spring 2011
... a constant source of comment. At the end of 1949 Chargaff noted that ‘‘A comparison of the molar proportions [of the bases] reveals certain striking, but perhaps meaningless, regularities’’. Early in 1950, he wrote ‘‘It is noteworthy, although possibly no more than accidental, that in all desoxypent ...
... a constant source of comment. At the end of 1949 Chargaff noted that ‘‘A comparison of the molar proportions [of the bases] reveals certain striking, but perhaps meaningless, regularities’’. Early in 1950, he wrote ‘‘It is noteworthy, although possibly no more than accidental, that in all desoxypent ...
Document
... (k) explain how plasmids may be taken up by bacterial cells in order to produce a transgenic microorganism that can express a desired gene product; (l) describe the advantage to microorganisms of the capacity to take up plasmid DNA from the environment; (m) outline how genetic markers in plasmids ca ...
... (k) explain how plasmids may be taken up by bacterial cells in order to produce a transgenic microorganism that can express a desired gene product; (l) describe the advantage to microorganisms of the capacity to take up plasmid DNA from the environment; (m) outline how genetic markers in plasmids ca ...
Ch. 13.1: BIOTECHNOLOGY
... cuts; unpaired bases; useful b/c they h-bond w/ complimentary bases in other fragments. Helps to “sew” fragments together & make recomb. DNA. ...
... cuts; unpaired bases; useful b/c they h-bond w/ complimentary bases in other fragments. Helps to “sew” fragments together & make recomb. DNA. ...
Slide
... family of related members often with related function. Finding these genes, or a gene from one species in another, can be done by differential hybridization using sequences from the known gene as DNA hybridization probes for the unknown genes. ...
... family of related members often with related function. Finding these genes, or a gene from one species in another, can be done by differential hybridization using sequences from the known gene as DNA hybridization probes for the unknown genes. ...
practical sheet
... Depending of the performance of your computer, we may have to reduce the initial number of genes at play in order to perform your analysis comfortably (that is, by not waiting too much for R). — For each gene, test the difference in the mean between the two groups (ALL/AML), with a t-test or a Wilco ...
... Depending of the performance of your computer, we may have to reduce the initial number of genes at play in order to perform your analysis comfortably (that is, by not waiting too much for R). — For each gene, test the difference in the mean between the two groups (ALL/AML), with a t-test or a Wilco ...
PATENT PROTECTION FOR GENE SEQUENCES WHAT IS
... number of producers and DNA samples have to be sent to Myriad in the U.S. for processing as well as establishing a huge databank about people at cancer risk. The latter may even involve issues of data protection and privacy. • Scientists are warning that the Myriad test does not cover newly discover ...
... number of producers and DNA samples have to be sent to Myriad in the U.S. for processing as well as establishing a huge databank about people at cancer risk. The latter may even involve issues of data protection and privacy. • Scientists are warning that the Myriad test does not cover newly discover ...
Correlation of transcriptomic and phenotypic data in dairy cows
... • An awesome data set as both gene expression and phenotypic data available for ~ 350 dairy cows. • Our objective was to determine if any genes had expression that was significantly correlated with any of the phenotypes. • Essentially a data-mining exercise, however because of the large number of sa ...
... • An awesome data set as both gene expression and phenotypic data available for ~ 350 dairy cows. • Our objective was to determine if any genes had expression that was significantly correlated with any of the phenotypes. • Essentially a data-mining exercise, however because of the large number of sa ...
Notes on Haldane`s mapping function and physical and recomb maps
... You can see that for small values of recombination (say less than about 0.2) the two approaches give similar mapping distances. As r increases, there is an increasing difference between the two mapping approaches. ...
... You can see that for small values of recombination (say less than about 0.2) the two approaches give similar mapping distances. As r increases, there is an increasing difference between the two mapping approaches. ...
Lect19_TumorSeq
... Mutations in the Tumor Genome • Help us identify important genes for tumorigenesis and cancer progression • Drivers – a.k.a gatekeepers, mutations that cause and accelerate cancers • Passengers – Accidental by-products and thwarted DNA-repair mechanisms • Recurrent mutations on genes or pathways ar ...
... Mutations in the Tumor Genome • Help us identify important genes for tumorigenesis and cancer progression • Drivers – a.k.a gatekeepers, mutations that cause and accelerate cancers • Passengers – Accidental by-products and thwarted DNA-repair mechanisms • Recurrent mutations on genes or pathways ar ...
How Environmental Factors Influence Transcription (PowerPoint)
... • Gather into groups • Collect an envelope containing word strips • Arrange the molecular events in the order that they occur in the cell • You have 5 minutes…GO! ...
... • Gather into groups • Collect an envelope containing word strips • Arrange the molecular events in the order that they occur in the cell • You have 5 minutes…GO! ...
Genomics: A new Revolution in Science
... • But because only a few regions of DNA actively encode life functions, the real difference between one person and another is only 0.0003 percent ...
... • But because only a few regions of DNA actively encode life functions, the real difference between one person and another is only 0.0003 percent ...
assignment DNA - UniMAP Portal
... 4. Why are mutation and recombination important in the process of natural selection and the evolution of organisms? ...
... 4. Why are mutation and recombination important in the process of natural selection and the evolution of organisms? ...
Gut Flora: More Important than we Thought
... There might be none Many genes code for more than one protein Maybe there are not that many proteins/traits ...
... There might be none Many genes code for more than one protein Maybe there are not that many proteins/traits ...
Gene Cloning
... all or part of a macromolecule (such as DNA or an antibody) • An individual grown from a single somatic cell of its parent & genetically identical to it www.m-w/cgi-bin/dictionary ...
... all or part of a macromolecule (such as DNA or an antibody) • An individual grown from a single somatic cell of its parent & genetically identical to it www.m-w/cgi-bin/dictionary ...
One system, one workflow, powerful new sequencing applications
... characterization of genomic structure. Unlock critical genetic information for variants in heritable disorders, and discover key alterations in cancer. ...
... characterization of genomic structure. Unlock critical genetic information for variants in heritable disorders, and discover key alterations in cancer. ...
Applications of genomics in Plant Breeding
... statistically analyze the data for mostly 454 and Illumina platforms (Tongwu, et al., 2011, A, et al., 2009 ) Alignment of genomes to reference genome, commonly referred to as De Novo genome assembly, is the most important step in making sense out of NGS data (Flicek & Birney, 2009) Short reads is a ...
... statistically analyze the data for mostly 454 and Illumina platforms (Tongwu, et al., 2011, A, et al., 2009 ) Alignment of genomes to reference genome, commonly referred to as De Novo genome assembly, is the most important step in making sense out of NGS data (Flicek & Birney, 2009) Short reads is a ...
Gene discovery within the planctomycete division of the domain
... [1-6]. Planctomycetes are currently represented by only a few cultured and characterized heterotrophic members ...
... [1-6]. Planctomycetes are currently represented by only a few cultured and characterized heterotrophic members ...
Human Heredity - mccombsscience
... For a long time, reading the DNA sequences in the human genome seemed impossible (the smallest chromosome contains nearly 50 million base pairs!) ...
... For a long time, reading the DNA sequences in the human genome seemed impossible (the smallest chromosome contains nearly 50 million base pairs!) ...
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.