The Experts below are selected from a list of 222 Experts worldwide ranked by ideXlab platform
Roger L. Dawkins - One of the best experts on this subject based on the ideXlab platform.
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Genomic analysis reveals a duplication of eight rather than seven short consensus repeats in primate CR1 and CR1L: evidence for an additional set shared between CR1 and CR2
Immunogenetics, 2004Co-Authors: Craig A. Mclure, Joseph F. Williamson, Brent J. Stewart, Peter J. Keating, Roger L. DawkinsAbstract:We report the discovery of previously unrecognised short consensus repeats (SCRs) within human and chimpanzee CR1 and CR1L . Analysis of available genomic, protein and expression databases suggests that these are actually genomic remnants of SCRs previously reported in other complement control proteins (CCPs). Comparison with the Nucleotide Motifs of the 11 defined subfamilies of SCRs justifies the designation g-like because of the close similarity to the g subfamily found in CR2 and MCP . To date, we have identified five such SCRs in human and chimpanzee CR1 , one in human and chimpanzee CR1L , but none in either rat or mouse Crry in keeping with the number of internal duplications of the long homologous repeat (LHR) found in CR1 and CR1L . In fact, at the genomic level, the ancestral LHR must have contained eight SCRs rather than seven as previously thought. Since g-like SCRs are found immediately downstream of d SCRs, we suggest that there must have been a functional dg set which has been retained by CR2 and MCP but which is degenerate in CR1 or CR1L . Interestingly, dg is also present in the CR2 component of mouse CR1 . The degeneration of the g SCR must have occurred prior to the formation of primate CR1L and prior to the duplication events which resulted in primate CR1 . In this context, the apparent conservation of g-like SCRs may be surprising and may suggest the existence of mechanisms unrelated to protein coding. These results provide examples of the many processes which have contributed to the evolution of the extensive repertoire of CCPs.
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Genomic analysis reveals a duplication of eight rather than seven short consensus repeats in primate CR1 and CR1L: evidence for an additional set shared between CR1 and CR2
Immunogenetics, 2004Co-Authors: Craig A. Mclure, Joseph F. Williamson, Brent J. Stewart, Peter J. Keating, Roger L. DawkinsAbstract:We report the discovery of previously unrecognised short consensus repeats (SCRs) within human and chimpanzee CR1 and CR1L. Analysis of available genomic, protein and expression databases suggests that these are actually genomic remnants of SCRs previously reported in other complement control proteins (CCPs). Comparison with the Nucleotide Motifs of the 11 defined subfamilies of SCRs justifies the designation g-like because of the close similarity to the g subfamily found in CR2 and MCP.
Craig A. Mclure - One of the best experts on this subject based on the ideXlab platform.
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Genomic analysis reveals a duplication of eight rather than seven short consensus repeats in primate CR1 and CR1L: evidence for an additional set shared between CR1 and CR2
Immunogenetics, 2004Co-Authors: Craig A. Mclure, Joseph F. Williamson, Brent J. Stewart, Peter J. Keating, Roger L. DawkinsAbstract:We report the discovery of previously unrecognised short consensus repeats (SCRs) within human and chimpanzee CR1 and CR1L . Analysis of available genomic, protein and expression databases suggests that these are actually genomic remnants of SCRs previously reported in other complement control proteins (CCPs). Comparison with the Nucleotide Motifs of the 11 defined subfamilies of SCRs justifies the designation g-like because of the close similarity to the g subfamily found in CR2 and MCP . To date, we have identified five such SCRs in human and chimpanzee CR1 , one in human and chimpanzee CR1L , but none in either rat or mouse Crry in keeping with the number of internal duplications of the long homologous repeat (LHR) found in CR1 and CR1L . In fact, at the genomic level, the ancestral LHR must have contained eight SCRs rather than seven as previously thought. Since g-like SCRs are found immediately downstream of d SCRs, we suggest that there must have been a functional dg set which has been retained by CR2 and MCP but which is degenerate in CR1 or CR1L . Interestingly, dg is also present in the CR2 component of mouse CR1 . The degeneration of the g SCR must have occurred prior to the formation of primate CR1L and prior to the duplication events which resulted in primate CR1 . In this context, the apparent conservation of g-like SCRs may be surprising and may suggest the existence of mechanisms unrelated to protein coding. These results provide examples of the many processes which have contributed to the evolution of the extensive repertoire of CCPs.
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Genomic analysis reveals a duplication of eight rather than seven short consensus repeats in primate CR1 and CR1L: evidence for an additional set shared between CR1 and CR2
Immunogenetics, 2004Co-Authors: Craig A. Mclure, Joseph F. Williamson, Brent J. Stewart, Peter J. Keating, Roger L. DawkinsAbstract:We report the discovery of previously unrecognised short consensus repeats (SCRs) within human and chimpanzee CR1 and CR1L. Analysis of available genomic, protein and expression databases suggests that these are actually genomic remnants of SCRs previously reported in other complement control proteins (CCPs). Comparison with the Nucleotide Motifs of the 11 defined subfamilies of SCRs justifies the designation g-like because of the close similarity to the g subfamily found in CR2 and MCP.
Elisha D O Roberson - One of the best experts on this subject based on the ideXlab platform.
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Motif scraper: a cross-platform, open-source tool for identifying degenerate Nucleotide motif matches in FASTA files
Bioinformatics, 2018Co-Authors: Elisha D O RobersonAbstract:Many genomic features are defined not by exact sequence matches, but by degenerate Nucleotide Motifs that represent multiple compatible matches. While there are databases cataloging genomic features, such as the location of transcription factor Motifs, for commonly used model species, identifying the locations of novel Motifs, known Motifs in non-model genomes, or known Motifs in personal whole-genomes is difficult. I designed motif scraper to overcome this limitation, allowing for efficient, multiprocessor motif searches in any FASTA file. The motif scraper package (MIT license) is available via PyPI, and the Python source is available on GitHub at https://github.com/RobersonLab/motif_scraper.
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Motif Scraper: A cross-platform, open-source tool for identifying degenerate Nucleotide motif matches in FASTA files
bioRxiv, 2018Co-Authors: Elisha D O RobersonAbstract:Many genomic features are defined not by exact sequence matches, but by degenerate Nucleotide Motifs that represent multiple compatible matches. While there are databases cataloging genomic features, such as the location of transcription factor Motifs, for commonly used model species, identifying the locations of novel Motifs, known Motifs in non-model genomes, or known Motifs in personal whole-genomes is difficult. I designed motif scraper to overcome this limitation, allowing for efficient, multiprocessor motif searches in any FASTA file.
Udaykumar Ranga - One of the best experts on this subject based on the ideXlab platform.
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CSB - A pattern matching algorithm for codon optimization and CpG motif-engineering in DNA expression vectors
Proceedings. IEEE Computer Society Bioinformatics Conference, 2003Co-Authors: Ravi Vijaya Satya, Amar Mukherjee, Udaykumar RangaAbstract:Codon optimization enhances the efficiency of DNA expression vectors used in DNA vaccination and gene therapy by increasing protein expression. Additionally, certain Nucleotide Motifs have experimentally been shown to be immuno-stimulatory while certain others immuno-suppressive. In this paper, we present algorithms to locate a given set of immuno-modulatory Motifs in the DNA expression vectors corresponding to a given amino acid sequence and maximize or minimize the number and the context of the immuno-modulatory Motifs in the DNA expression vectors. The main contribution is to use multiple pattern matching algorithms to synthesize a DNA sequence for a given amino acid sequence and a graph theoretic approach for finding the longest weighted path in a directed graph that will maximize or minimize certain Motifs. This is achieved using O(n/sup 2/) time, where n is the length of the amino acid sequence. Based on this, we develop a software tool.
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A pattern matching algorithm for codon optimization and CpG motif-engineering in DNA expression vectors
Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003, 2003Co-Authors: Ravi Vijaya Satya, Amar Mukherjee, Udaykumar RangaAbstract:Codon optimization enhances the efficiency of DNA expression vectors used in DNA vaccination and gene therapy by increasing protein expression. Additionally, certain Nucleotide Motifs have experimentally been shown to be immuno-stimulatory while certain others immuno-suppressive. In this paper, we present algorithms to locate a given set of immuno-modulatory Motifs in the DNA expression vectors corresponding to a given amino acid sequence and maximize or minimize the number and the context of the immuno-modulatory Motifs in the DNA expression vectors. The main contribution is to use multiple pattern matching algorithms to synthesize a DNA sequence for a given amino acid sequence and a graph theoretic approach for finding the longest weighted path in a directed graph that will maximize or minimize certain Motifs. This is achieved using O(n2) time, where n is the length of the amino acid sequence. Based on this, we develop a software tool.
Peter J. Keating - One of the best experts on this subject based on the ideXlab platform.
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Genomic analysis reveals a duplication of eight rather than seven short consensus repeats in primate CR1 and CR1L: evidence for an additional set shared between CR1 and CR2
Immunogenetics, 2004Co-Authors: Craig A. Mclure, Joseph F. Williamson, Brent J. Stewart, Peter J. Keating, Roger L. DawkinsAbstract:We report the discovery of previously unrecognised short consensus repeats (SCRs) within human and chimpanzee CR1 and CR1L . Analysis of available genomic, protein and expression databases suggests that these are actually genomic remnants of SCRs previously reported in other complement control proteins (CCPs). Comparison with the Nucleotide Motifs of the 11 defined subfamilies of SCRs justifies the designation g-like because of the close similarity to the g subfamily found in CR2 and MCP . To date, we have identified five such SCRs in human and chimpanzee CR1 , one in human and chimpanzee CR1L , but none in either rat or mouse Crry in keeping with the number of internal duplications of the long homologous repeat (LHR) found in CR1 and CR1L . In fact, at the genomic level, the ancestral LHR must have contained eight SCRs rather than seven as previously thought. Since g-like SCRs are found immediately downstream of d SCRs, we suggest that there must have been a functional dg set which has been retained by CR2 and MCP but which is degenerate in CR1 or CR1L . Interestingly, dg is also present in the CR2 component of mouse CR1 . The degeneration of the g SCR must have occurred prior to the formation of primate CR1L and prior to the duplication events which resulted in primate CR1 . In this context, the apparent conservation of g-like SCRs may be surprising and may suggest the existence of mechanisms unrelated to protein coding. These results provide examples of the many processes which have contributed to the evolution of the extensive repertoire of CCPs.
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Genomic analysis reveals a duplication of eight rather than seven short consensus repeats in primate CR1 and CR1L: evidence for an additional set shared between CR1 and CR2
Immunogenetics, 2004Co-Authors: Craig A. Mclure, Joseph F. Williamson, Brent J. Stewart, Peter J. Keating, Roger L. DawkinsAbstract:We report the discovery of previously unrecognised short consensus repeats (SCRs) within human and chimpanzee CR1 and CR1L. Analysis of available genomic, protein and expression databases suggests that these are actually genomic remnants of SCRs previously reported in other complement control proteins (CCPs). Comparison with the Nucleotide Motifs of the 11 defined subfamilies of SCRs justifies the designation g-like because of the close similarity to the g subfamily found in CR2 and MCP.
