Algorithm to extract REP sequences Pattern
... III. Determination of short tandem repeats (STRs) IV. Analysis of gene expression data ...
... III. Determination of short tandem repeats (STRs) IV. Analysis of gene expression data ...
Presentation: Computation to Solve Problems
... III. Determination of short tandem repeats (STRs) IV. Analysis of gene expression data ...
... III. Determination of short tandem repeats (STRs) IV. Analysis of gene expression data ...
Molecular Phylogenetic Analysis Among Bryophytes and
... for the original LogDet distance by Steel (1994). To utilize the power of the paralinear or LogDet distance, it is important to use only those sites that evolve at the same rate. If constant sites are included, the phylogeny based on the LogDet distance may fall into the same topology as that inferr ...
... for the original LogDet distance by Steel (1994). To utilize the power of the paralinear or LogDet distance, it is important to use only those sites that evolve at the same rate. If constant sites are included, the phylogeny based on the LogDet distance may fall into the same topology as that inferr ...
Genes Identified by Visible Mutant Phenotypes Show Increased Bias
... nonsyntenic positions within the last 70 million years [24]. A recent study in Drosophila found that knockouts of recently inserted – within the last 35 million years – and ancient syntenically conserved genes produced lethal phenotypes at statistically similar rates [25]. Genes belonging to the gra ...
... nonsyntenic positions within the last 70 million years [24]. A recent study in Drosophila found that knockouts of recently inserted – within the last 35 million years – and ancient syntenically conserved genes produced lethal phenotypes at statistically similar rates [25]. Genes belonging to the gra ...
Genes
... fragmentation of an ortholog into two smaller ORFs. For the bottom most 11L ortholog showed in the above diagram is showed to have several large in-frame deletions in the gene when compared to the aligned genomes. Fusion between MGF 110 – 13L amino terminus and 11L carboxy terminus separated by dele ...
... fragmentation of an ortholog into two smaller ORFs. For the bottom most 11L ortholog showed in the above diagram is showed to have several large in-frame deletions in the gene when compared to the aligned genomes. Fusion between MGF 110 – 13L amino terminus and 11L carboxy terminus separated by dele ...
Diapositive 1 - Institut Pasteur
... ● Although deletion analyses of PE/PPE genes were accompanied with phenotypic characteristics, the detailed molecular mechanisms responsible for the observed effects remain to be demonstrated ...
... ● Although deletion analyses of PE/PPE genes were accompanied with phenotypic characteristics, the detailed molecular mechanisms responsible for the observed effects remain to be demonstrated ...
ppt - Chair of Computational Biology
... observations. The process evolves in some dimension, often time, though not necessarily. The model is parameterized with probabilities governing the state at a time t + 1, given that one knows the previous states. Markov assumptions are used to truncate the dependency of having to know the entire hi ...
... observations. The process evolves in some dimension, often time, though not necessarily. The model is parameterized with probabilities governing the state at a time t + 1, given that one knows the previous states. Markov assumptions are used to truncate the dependency of having to know the entire hi ...
Characterization of the ves Gene, Which is Expressed at a Low
... Marahiel, 1998). The family members seem to share common functional properties because a growth defect at low temperature was not observed until four csp genes (cspA, cspB, cspE and cspG) were deleted, and the defect was suppressed by most of the family members (Xia et al., 2001). As has been demons ...
... Marahiel, 1998). The family members seem to share common functional properties because a growth defect at low temperature was not observed until four csp genes (cspA, cspB, cspE and cspG) were deleted, and the defect was suppressed by most of the family members (Xia et al., 2001). As has been demons ...
DNA interference: DNA-induced gene silencing in the
... recognizes and cleaves the target mRNA [3]. It is now known that RNAi operates in a broad range of organisms from fungi to vertebrates [4,5]. On the other hand, DNA interference (DNAi) has also been reported in a few species of plants, ciliates and archaeans. In tobacco and Adiantum, introduction of ...
... recognizes and cleaves the target mRNA [3]. It is now known that RNAi operates in a broad range of organisms from fungi to vertebrates [4,5]. On the other hand, DNA interference (DNAi) has also been reported in a few species of plants, ciliates and archaeans. In tobacco and Adiantum, introduction of ...
The genome-scale interplay amongst xenogene silencing
... We had previously constructed a double Δhns-stpA deletion mutant in E. coli K12 MG1655 using homologous recombination (6). The transcriptome of this strain––relative to the wild type––during mid-exponential phase in LB medium exhibits an increase in the expression of many A+T-rich genes, consistent ...
... We had previously constructed a double Δhns-stpA deletion mutant in E. coli K12 MG1655 using homologous recombination (6). The transcriptome of this strain––relative to the wild type––during mid-exponential phase in LB medium exhibits an increase in the expression of many A+T-rich genes, consistent ...
Jounral of Bacteriology
... sequence reads (5.76 ⫻ coverage) from our shot gun approach (see Materials and Methods). The total length of the nonredundant sequence formed by all contigs was 3,818 kb, which is slightly less than the size of the B. subtilis 168 genome of 4,214 kb (16). We identified 2,980 genes (72.7%) on the FZB ...
... sequence reads (5.76 ⫻ coverage) from our shot gun approach (see Materials and Methods). The total length of the nonredundant sequence formed by all contigs was 3,818 kb, which is slightly less than the size of the B. subtilis 168 genome of 4,214 kb (16). We identified 2,980 genes (72.7%) on the FZB ...
Chromatin Domain Boundaries: Defining the Functional Domains in
... Eukaryotic genome is packaged in the nucleus with the help of several proteins. While this packaging is needed to accommodate the large genome within the nuclear volume it also has functional consequences. It is well known that enhancers can act over a long distance to regulate expression of genes, ...
... Eukaryotic genome is packaged in the nucleus with the help of several proteins. While this packaging is needed to accommodate the large genome within the nuclear volume it also has functional consequences. It is well known that enhancers can act over a long distance to regulate expression of genes, ...
Genome analysis of Desulfotomaculum gibsoniae strain
... Keywords: spore-forming anaerobes, sulfate reduction, autotrophic, anaerobic degradation of aromatic compounds, complete oxidizer, Peptococcaceae, Clostridiales Desulfotomaculum gibsoniae is a mesophilic member of the polyphyletic spore-forming genus Desulfotomaculum within the family Peptococcaceae ...
... Keywords: spore-forming anaerobes, sulfate reduction, autotrophic, anaerobic degradation of aromatic compounds, complete oxidizer, Peptococcaceae, Clostridiales Desulfotomaculum gibsoniae is a mesophilic member of the polyphyletic spore-forming genus Desulfotomaculum within the family Peptococcaceae ...
Karyotype, ploidy, and gene dosage
... means of the IV-X fusion chromosome, mnT12, and also by using a meiotic mutant, him-6 (Sigurdson et al., 1984). The triplo-IV animals have surprisingly normal appearance and viability, although they produce 50% fewer progeny than normal hermaphrodites. The inviability of most of the other possible a ...
... means of the IV-X fusion chromosome, mnT12, and also by using a meiotic mutant, him-6 (Sigurdson et al., 1984). The triplo-IV animals have surprisingly normal appearance and viability, although they produce 50% fewer progeny than normal hermaphrodites. The inviability of most of the other possible a ...
The role of duplications in the evolution of genomes highlights the
... triploids, generally considered to be an evolutionary dead-end as they tend to produce aneuploid gametes owing to problems of chromosomal pairing and segregation during meiosis. However, it has been demonstrated that triploids can generate euploid (haploid, diploid, triploid) gametes at a low rate [ ...
... triploids, generally considered to be an evolutionary dead-end as they tend to produce aneuploid gametes owing to problems of chromosomal pairing and segregation during meiosis. However, it has been demonstrated that triploids can generate euploid (haploid, diploid, triploid) gametes at a low rate [ ...
Genome analysis of Desulfotomaculum gibsoniae strain
... Keywords: spore-forming anaerobes, sulfate reduction, autotrophic, anaerobic degradation of aromatic compounds, complete oxidizer, Peptococcaceae, Clostridiales Desulfotomaculum gibsoniae is a mesophilic member of the polyphyletic spore-forming genus Desulfotomaculum within the family Peptococcaceae ...
... Keywords: spore-forming anaerobes, sulfate reduction, autotrophic, anaerobic degradation of aromatic compounds, complete oxidizer, Peptococcaceae, Clostridiales Desulfotomaculum gibsoniae is a mesophilic member of the polyphyletic spore-forming genus Desulfotomaculum within the family Peptococcaceae ...
PPT - Blumberg Lab
... • Loss-of-function analysis is the most powerful way to identify gene function – Direct link between genotype and phenotype – Forward vs reverse genetics • Forward genetics-> random mutagenesis, then phenotypic analysis – Identity of gene involved not known at the start • Reverse genetics -> associa ...
... • Loss-of-function analysis is the most powerful way to identify gene function – Direct link between genotype and phenotype – Forward vs reverse genetics • Forward genetics-> random mutagenesis, then phenotypic analysis – Identity of gene involved not known at the start • Reverse genetics -> associa ...
Barley Cbf3 Gene Identification, Expression Pattern, and Map Location
... of the HvCbf3 gene, we used real-time reverse transcription PCR. Total RNA was isolated from barley seedling shoots sampled at different times throughout a chilling or ABA treatment. For comparison, mRNAs from the same RNA samples were amplified with primers specific for known chilling- and ABAinduc ...
... of the HvCbf3 gene, we used real-time reverse transcription PCR. Total RNA was isolated from barley seedling shoots sampled at different times throughout a chilling or ABA treatment. For comparison, mRNAs from the same RNA samples were amplified with primers specific for known chilling- and ABAinduc ...
Two Cyp19 (P450 Aromatase) Genes on Duplicated Zebrafish
... AF004521. The other sequence in GenBank (accession number AF120031) is a partial sequence. It differs from our cyp19b (accession number AF183908) in the overlapped region by three bases, resulting in a change of one amino acid. There is an overall 60% sequence identity between zebrafish Cyp19a and C ...
... AF004521. The other sequence in GenBank (accession number AF120031) is a partial sequence. It differs from our cyp19b (accession number AF183908) in the overlapped region by three bases, resulting in a change of one amino acid. There is an overall 60% sequence identity between zebrafish Cyp19a and C ...
Annotation report - GEP Community Server
... 3. Alignment between the submitted model and the D. melanogaster ortholog Show an alignment between the protein sequence for your gene model and the protein sequence from the putative D. melanogaster ortholog. You can either use the protein alignment generated by the Gene Model Checker (available th ...
... 3. Alignment between the submitted model and the D. melanogaster ortholog Show an alignment between the protein sequence for your gene model and the protein sequence from the putative D. melanogaster ortholog. You can either use the protein alignment generated by the Gene Model Checker (available th ...
AP & Regents Biology
... to learn biology Using computers to study primary biological data (genomes, proteins, other databases) students learn biology as a dynamic process of interpreting complex data students can reproduce current scientific work & ask new questions ...
... to learn biology Using computers to study primary biological data (genomes, proteins, other databases) students learn biology as a dynamic process of interpreting complex data students can reproduce current scientific work & ask new questions ...
Validated preCRMs
... regulatory regions of Ciona (Johnson et al. 2004). Another approach using aligned genomic sequences to predict CRMs is the computation of regulatory potential (RP), which captures context and pattern information in addition to conservation (Elnitski et al. 2003; Kolbe et al. 2004; Taylor et al. 2006 ...
... regulatory regions of Ciona (Johnson et al. 2004). Another approach using aligned genomic sequences to predict CRMs is the computation of regulatory potential (RP), which captures context and pattern information in addition to conservation (Elnitski et al. 2003; Kolbe et al. 2004; Taylor et al. 2006 ...
pdf
... To facilitate the generation of Plac-based NotI-expression cassettes in cases of deleterious gene dosage effects to the E. coli host cell, we inserted the 0.4-kb NotI lacZa fragment from plasmid pNot18 into the NotI digested low-copy-number pCK01 vector [4] (Fig. 1). The resultant plasmid, pSJP18Not ...
... To facilitate the generation of Plac-based NotI-expression cassettes in cases of deleterious gene dosage effects to the E. coli host cell, we inserted the 0.4-kb NotI lacZa fragment from plasmid pNot18 into the NotI digested low-copy-number pCK01 vector [4] (Fig. 1). The resultant plasmid, pSJP18Not ...
Sequences 5` to Translation Start Regulate
... petunia rbcS gene). Schematic illustrations of the 5'-flanking regions of SSU301 and SSU911 are shown in Figure 1. These serve to simplify the region of interest and show the restriction endonuclease sites used in the cloning steps, The three conserved blocks of nucleotide sequence present in SSU301 ...
... petunia rbcS gene). Schematic illustrations of the 5'-flanking regions of SSU301 and SSU911 are shown in Figure 1. These serve to simplify the region of interest and show the restriction endonuclease sites used in the cloning steps, The three conserved blocks of nucleotide sequence present in SSU301 ...
Transposable element
A transposable element (TE or transposon) is a DNA sequence that can change its position within the genome, sometimes creating or reversing mutations and altering the cell's genome size. Transposition often results in duplication of the TE. Barbara McClintock's discovery of these jumping genes earned her a Nobel prize in 1983.TEs make up a large fraction of the C-value of eukaryotic cells. There are at least two classes of TEs: class I TEs generally function via reverse transcription, while class II TEs encode the protein transposase, which they require for insertion and excision, and some of these TEs also encode other proteins. It has been shown that TEs are important in genome function and evolution. In Oxytricha, which has a unique genetic system, they play a critical role in development. They are also very useful to researchers as a means to alter DNA inside a living organism.