Ch15-Computational_Approaches_in_Comparative_Genomics
... By comparing genomes to gain a better understanding of the similarities & differences between genomes over evolutionary times ...
... By comparing genomes to gain a better understanding of the similarities & differences between genomes over evolutionary times ...
What happened to my genes? Insights on gene family dynamics
... The usual strategy to identify gene families consists in detecting significant sequence similarities in gene or protein sequences. This method is inherently biased towards the detection of families that evolve mainly through local mutations rather than domain shuffling. As Song et al. (2008) make it ...
... The usual strategy to identify gene families consists in detecting significant sequence similarities in gene or protein sequences. This method is inherently biased towards the detection of families that evolve mainly through local mutations rather than domain shuffling. As Song et al. (2008) make it ...
MCB 371/372 homology homology vs analogy
... Paralogs: “deepest” bifurcation in molecular tree reflects gene duplication. The study of paralogs and their distribution in genomes provides clues on the way genomes evolved. Gen and genome duplication have emerged as the most important pathway to molecular innovation, including the evolution of de ...
... Paralogs: “deepest” bifurcation in molecular tree reflects gene duplication. The study of paralogs and their distribution in genomes provides clues on the way genomes evolved. Gen and genome duplication have emerged as the most important pathway to molecular innovation, including the evolution of de ...
Kelly PD, Chu F, Woods IG, Ngo‑Hazelett P, Cardozo T, Huang H
... panel and in previous work. The HS panel map assigned 591 of 593 SSLPs to the same linkage groups as Shimoda et al. (1999). Of these 591 markers, there were eight cases where the order of closely spaced markers differed between the two maps. Because closely spaced markers are separated by few recomb ...
... panel and in previous work. The HS panel map assigned 591 of 593 SSLPs to the same linkage groups as Shimoda et al. (1999). Of these 591 markers, there were eight cases where the order of closely spaced markers differed between the two maps. Because closely spaced markers are separated by few recomb ...
BioinformaIcs Journal Club
... This special issue reflects the recent advances in the field of environmental genomics and exposes the aPrac)ve prospects in the light of the new, rapidly-‐evolving tools that are next genera)on seque ...
... This special issue reflects the recent advances in the field of environmental genomics and exposes the aPrac)ve prospects in the light of the new, rapidly-‐evolving tools that are next genera)on seque ...
ppt
... Paralogs: “deepest” bifurcation in molecular tree reflects gene duplication. The study of paralogs and their distribution in genomes provides clues on the way genomes evolved. Gen and genome duplication have emerged as the most important pathway to molecular innovation, including the evolution of de ...
... Paralogs: “deepest” bifurcation in molecular tree reflects gene duplication. The study of paralogs and their distribution in genomes provides clues on the way genomes evolved. Gen and genome duplication have emerged as the most important pathway to molecular innovation, including the evolution of de ...
The dawn of evolutionary genome engineering
... Since the split of the two lineages 200 million years ago, the free-living ancestor lost 75% of its genome, including mobile genetic elements30. Buchnera spp. now contain ~580 genes, which shows that such a small number of genes is sufficient to maintain cellular life under a constant intracellular ...
... Since the split of the two lineages 200 million years ago, the free-living ancestor lost 75% of its genome, including mobile genetic elements30. Buchnera spp. now contain ~580 genes, which shows that such a small number of genes is sufficient to maintain cellular life under a constant intracellular ...
A Novel Chimeric Low-Molecular-Weight Glutenin
... Phylogenetic analysis among LMW-GS and other storage protein genes: The 27 gene sequences coding for LMW-GS, gliadins, and hordeins from GenBank were used to construct a homology tree, including 3 LMW-s-type, 12 LMW-m-type, and 5 LMW-i-type glutenin genes as well as 4 gliadins and 3 hordein genes fr ...
... Phylogenetic analysis among LMW-GS and other storage protein genes: The 27 gene sequences coding for LMW-GS, gliadins, and hordeins from GenBank were used to construct a homology tree, including 3 LMW-s-type, 12 LMW-m-type, and 5 LMW-i-type glutenin genes as well as 4 gliadins and 3 hordein genes fr ...
The Genome of Deep-Sea Vent Chemolithoautotroph
... chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. This gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. It has 14 methyl-accepting chemota ...
... chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. This gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. It has 14 methyl-accepting chemota ...
Figure 1 - York College of Pennsylvania
... •PPT1 is a lysosomal enzyme that plays a major role in the degradation of lipid-modified proteins. •How PPT1 deficiency leads to selective central nervous system degeneration is unclear. ...
... •PPT1 is a lysosomal enzyme that plays a major role in the degradation of lipid-modified proteins. •How PPT1 deficiency leads to selective central nervous system degeneration is unclear. ...
RESEARCH ARTICLES
... CP001621] (10). The other was a strain created by transplantation of a genome that had been cloned and engineered in yeast, YCpMmyc1.1- typeIIIres [GenBank accession CP001668] (8). This project was critically dependent on the accuracy of these sequences. Although we believe that both finished M. myc ...
... CP001621] (10). The other was a strain created by transplantation of a genome that had been cloned and engineered in yeast, YCpMmyc1.1- typeIIIres [GenBank accession CP001668] (8). This project was critically dependent on the accuracy of these sequences. Although we believe that both finished M. myc ...
Greedy Algorithms And Genome Rearrangements
... have similar genomes, but their genes are ordered differently • ~245 rearrangements • Reversals • Fusions • Fissions • Translocation ...
... have similar genomes, but their genes are ordered differently • ~245 rearrangements • Reversals • Fusions • Fissions • Translocation ...
Myotonic dystrophy DM
... delayed onset form of their diseases, indicating that they may share mechanisms that postpone clinical expression until later in life. -Depending on where the unstable repeats are located within the gene, the repeat expansion disorders can be classified as having coding or noncoding mutations. ...
... delayed onset form of their diseases, indicating that they may share mechanisms that postpone clinical expression until later in life. -Depending on where the unstable repeats are located within the gene, the repeat expansion disorders can be classified as having coding or noncoding mutations. ...
Creating a Venn diagram and list for unique genes from RAST
... Go to rast.nmpdr.org Login to RAST (username: newmanlab password: 16srrna1) In the Jobs Overview window, find the organism you wish to focus on by searching the Name column and click View Details under Annotation Progress In the Job Details window, click Browse annotated genome in the SEED View ...
... Go to rast.nmpdr.org Login to RAST (username: newmanlab password: 16srrna1) In the Jobs Overview window, find the organism you wish to focus on by searching the Name column and click View Details under Annotation Progress In the Job Details window, click Browse annotated genome in the SEED View ...
The sequence of the tms transcript 2 locus of the A. tumefaciens
... junctions between the 2.7 Kb insert and the surrounding T-DNA (19, D. Sciaky, unpublished results) were inserted into M13 mp8 and mp9 vehicles developed by Messing and Vieira ( 2 0 ) . Other recombinant molecules used in this study were: (a) pDS236-l, containing a 560 bp Sal I fragment from the inte ...
... junctions between the 2.7 Kb insert and the surrounding T-DNA (19, D. Sciaky, unpublished results) were inserted into M13 mp8 and mp9 vehicles developed by Messing and Vieira ( 2 0 ) . Other recombinant molecules used in this study were: (a) pDS236-l, containing a 560 bp Sal I fragment from the inte ...
UCSC genome support forum
... actually to align larger regions of the reference assembly sequence. The suitability of BLAT depends on the size of the region that you're searching in addition to the amount of repetitive content. The tiles that Galt referred to are 11-base sequences that are overrepresented in the genome. In addit ...
... actually to align larger regions of the reference assembly sequence. The suitability of BLAT depends on the size of the region that you're searching in addition to the amount of repetitive content. The tiles that Galt referred to are 11-base sequences that are overrepresented in the genome. In addit ...
DNA SEQUENCING AND GENE STRUCTURE
... each DNA fragment. This permits the reaction to be used in the domain of greatest specificity: only the very initial stages of a chemical reaction are involved. The second step, the cleavage of the DNA strand, must be complete. Since the target has already been distinguished from the other bases alo ...
... each DNA fragment. This permits the reaction to be used in the domain of greatest specificity: only the very initial stages of a chemical reaction are involved. The second step, the cleavage of the DNA strand, must be complete. Since the target has already been distinguished from the other bases alo ...
On the Mutational Topology of the Bacterial Genome
... expected, meaning that the mutations are clustered. A more interesting departure from random is revealed by the locations of the mutations. In Figure 3A the 1625 BPSs are collected in 46 bins, each bin approximately 100 kb wide, starting at the origin of replication. The left and right sides of Figu ...
... expected, meaning that the mutations are clustered. A more interesting departure from random is revealed by the locations of the mutations. In Figure 3A the 1625 BPSs are collected in 46 bins, each bin approximately 100 kb wide, starting at the origin of replication. The left and right sides of Figu ...
1. Chromatin structure is based on successive levels of DNA packing
... • The different versions of each globin subunit are expressed at different times in development, fine-tuning function to changes in environment. – Within both the and families are sequences that are expressed during the embryonic, fetal, and/or adult stage of development. – The embryonic and fe ...
... • The different versions of each globin subunit are expressed at different times in development, fine-tuning function to changes in environment. – Within both the and families are sequences that are expressed during the embryonic, fetal, and/or adult stage of development. – The embryonic and fe ...
molecularevolution.rnaseq
... • Transcript quantification depends heavily in paired-end data • Transcript reconstruction is greatly improved when using ...
... • Transcript quantification depends heavily in paired-end data • Transcript reconstruction is greatly improved when using ...
Candidate gene screening using long-read sequencing
... Targeted sequencing and multiplexing Targeted sequencing workflow ...
... Targeted sequencing and multiplexing Targeted sequencing workflow ...
identifying parent-daughter relationships among duplicated genes1
... 1. Introduction Gene families are groups of genes with high sequence similarity that are derived from a common ancestor. The relationships between members of a gene family can be classified into orthology and paralogy based on their evolutionary history. Orthologs are pairs of genes that are diverge ...
... 1. Introduction Gene families are groups of genes with high sequence similarity that are derived from a common ancestor. The relationships between members of a gene family can be classified into orthology and paralogy based on their evolutionary history. Orthologs are pairs of genes that are diverge ...
SEGMENTAL VARIATION
... deal of human phenotypic variability including disease • Depth-of-coverage methods can detect many CNVs but not inversions and translocations. Variation from sample to sample limits sensitivity and specificity. ...
... deal of human phenotypic variability including disease • Depth-of-coverage methods can detect many CNVs but not inversions and translocations. Variation from sample to sample limits sensitivity and specificity. ...
Evolution of cis-regulatory elements in duplicated genes of yeast
... independent transcriptional regulatory elements of duplicates might also lead to functional diversification without having to invoke positive selection in the process (see also [4] for a similar neutral scenario). Given that degenerative mutations are more common than beneficial mutations and that m ...
... independent transcriptional regulatory elements of duplicates might also lead to functional diversification without having to invoke positive selection in the process (see also [4] for a similar neutral scenario). Given that degenerative mutations are more common than beneficial mutations and that m ...
Slcyt, a Newly Identified Sex-Linked Gene, Has
... generally accepted that no additions to this sex chromosome pair had occurred during its evolution, but that it evolved from a single ancestral autosome that can be identified by its gene content (Filatov 2005), but these new results show that at least part of the X near the PAR has recently been ad ...
... generally accepted that no additions to this sex chromosome pair had occurred during its evolution, but that it evolved from a single ancestral autosome that can be identified by its gene content (Filatov 2005), but these new results show that at least part of the X near the PAR has recently been ad ...
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.