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Stephan Frickenhaus - One of the best experts on this subject based on the ideXlab platform.
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STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive Microsatellite Marker design
BMC Bioinformatics, 2009Co-Authors: Lars Kraemer, Bánk Beszteri, Steffi Gäbler-schwarz, Christoph Held, Florian Leese, Christoph Mayer, Kevin Pöhlmann, Stephan FrickenhausAbstract:Background Microsatellites (MSs) are DNA Markers with high analytical power, which are widely used in population genetics, genetic mapping, and forensic studies. Currently available software solutions for high-throughput MS design (i) have shortcomings in detecting and distinguishing imperfect and perfect MSs, (ii) lack often necessary interactive design steps, and (iii) do not allow for the development of primers for multiplex amplifications. We present a set of new tools implemented as extensions to the S TADEN package, which provides the backbone functionality for flexible sequence analysis workflows. The possibility to assemble overlapping reads into unique contigs (provided by the base functionality of the S TADEN package) is important to avoid developing redundant Markers, a feature missing from most other similar tools. Results Our extensions to the S TADEN package provide the following functionality to facilitate Microsatellite (and also minisatellite) Marker design: The new modules (i) integrate the state-of-the-art tandem repeat detection and analysis software P HOBOS into workflows, (ii) provide two separate repeat detection steps – with different search criteria – one for masking repetitive regions during assembly of sequencing reads and the other for designing repeat-flanking primers for MS candidate loci, (iii) incorporate the widely used primer design program P RIMER 3 into S TADEN workflows, enabling the interactive design and visualization of flanking primers for Microsatellites, and (iv) provide the functionality to find optimal locus- and primer pair combinations for multiplex primer design. Furthermore, our extensions include a module for storing analysis results in an SQLite database, providing a transparent solution for data access from within as well as from outside of the S TADEN Package. Conclusion The S TADEN package is enhanced by our modules into a highly flexible, high-throughput, interactive tool for conventional and multiplex Microsatellite Marker design. It gives the user detailed control over the workflow, enabling flexible combinations of manual and automated analysis steps. The software is available under the OpenBSD License [ 1 , 2 ]. The high efficiency of our automated Marker design workflow has been confirmed in three Microsatellite development projects.
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stamp extensions to the staden sequence analysis package for high throughput interactive Microsatellite Marker design
BMC Bioinformatics, 2009Co-Authors: Lars Kraemer, Bánk Beszteri, Christoph Held, Florian Leese, Christoph Mayer, Kevin Pöhlmann, Steffi Gablerschwarz, Stephan FrickenhausAbstract:Microsatellites (MSs) are DNA Markers with high analytical power, which are widely used in population genetics, genetic mapping, and forensic studies. Currently available software solutions for high-throughput MS design (i) have shortcomings in detecting and distinguishing imperfect and perfect MSs, (ii) lack often necessary interactive design steps, and (iii) do not allow for the development of primers for multiplex amplifications. We present a set of new tools implemented as extensions to the STADEN package, which provides the backbone functionality for flexible sequence analysis workflows. The possibility to assemble overlapping reads into unique contigs (provided by the base functionality of the STADEN package) is important to avoid developing redundant Markers, a feature missing from most other similar tools. Our extensions to the STADEN package provide the following functionality to facilitate Microsatellite (and also minisatellite) Marker design: The new modules (i) integrate the state-of-the-art tandem repeat detection and analysis software PHOBOS into workflows, (ii) provide two separate repeat detection steps – with different search criteria – one for masking repetitive regions during assembly of sequencing reads and the other for designing repeat-flanking primers for MS candidate loci, (iii) incorporate the widely used primer design program PRIMER 3 into STADEN workflows, enabling the interactive design and visualization of flanking primers for Microsatellites, and (iv) provide the functionality to find optimal locus- and primer pair combinations for multiplex primer design. Furthermore, our extensions include a module for storing analysis results in an SQLite database, providing a transparent solution for data access from within as well as from outside of the STADEN Package. The STADEN package is enhanced by our modules into a highly flexible, high-throughput, interactive tool for conventional and multiplex Microsatellite Marker design. It gives the user detailed control over the workflow, enabling flexible combinations of manual and automated analysis steps. The software is available under the OpenBSD License [1, 2]. The high efficiency of our automated Marker design workflow has been confirmed in three Microsatellite development projects.
Florian Leese - One of the best experts on this subject based on the ideXlab platform.
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STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive Microsatellite Marker design
BMC Bioinformatics, 2009Co-Authors: Lars Kraemer, Bánk Beszteri, Steffi Gäbler-schwarz, Christoph Held, Florian Leese, Christoph Mayer, Kevin Pöhlmann, Stephan FrickenhausAbstract:Background Microsatellites (MSs) are DNA Markers with high analytical power, which are widely used in population genetics, genetic mapping, and forensic studies. Currently available software solutions for high-throughput MS design (i) have shortcomings in detecting and distinguishing imperfect and perfect MSs, (ii) lack often necessary interactive design steps, and (iii) do not allow for the development of primers for multiplex amplifications. We present a set of new tools implemented as extensions to the S TADEN package, which provides the backbone functionality for flexible sequence analysis workflows. The possibility to assemble overlapping reads into unique contigs (provided by the base functionality of the S TADEN package) is important to avoid developing redundant Markers, a feature missing from most other similar tools. Results Our extensions to the S TADEN package provide the following functionality to facilitate Microsatellite (and also minisatellite) Marker design: The new modules (i) integrate the state-of-the-art tandem repeat detection and analysis software P HOBOS into workflows, (ii) provide two separate repeat detection steps – with different search criteria – one for masking repetitive regions during assembly of sequencing reads and the other for designing repeat-flanking primers for MS candidate loci, (iii) incorporate the widely used primer design program P RIMER 3 into S TADEN workflows, enabling the interactive design and visualization of flanking primers for Microsatellites, and (iv) provide the functionality to find optimal locus- and primer pair combinations for multiplex primer design. Furthermore, our extensions include a module for storing analysis results in an SQLite database, providing a transparent solution for data access from within as well as from outside of the S TADEN Package. Conclusion The S TADEN package is enhanced by our modules into a highly flexible, high-throughput, interactive tool for conventional and multiplex Microsatellite Marker design. It gives the user detailed control over the workflow, enabling flexible combinations of manual and automated analysis steps. The software is available under the OpenBSD License [ 1 , 2 ]. The high efficiency of our automated Marker design workflow has been confirmed in three Microsatellite development projects.
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stamp extensions to the staden sequence analysis package for high throughput interactive Microsatellite Marker design
BMC Bioinformatics, 2009Co-Authors: Lars Kraemer, Bánk Beszteri, Christoph Held, Florian Leese, Christoph Mayer, Kevin Pöhlmann, Steffi Gablerschwarz, Stephan FrickenhausAbstract:Microsatellites (MSs) are DNA Markers with high analytical power, which are widely used in population genetics, genetic mapping, and forensic studies. Currently available software solutions for high-throughput MS design (i) have shortcomings in detecting and distinguishing imperfect and perfect MSs, (ii) lack often necessary interactive design steps, and (iii) do not allow for the development of primers for multiplex amplifications. We present a set of new tools implemented as extensions to the STADEN package, which provides the backbone functionality for flexible sequence analysis workflows. The possibility to assemble overlapping reads into unique contigs (provided by the base functionality of the STADEN package) is important to avoid developing redundant Markers, a feature missing from most other similar tools. Our extensions to the STADEN package provide the following functionality to facilitate Microsatellite (and also minisatellite) Marker design: The new modules (i) integrate the state-of-the-art tandem repeat detection and analysis software PHOBOS into workflows, (ii) provide two separate repeat detection steps – with different search criteria – one for masking repetitive regions during assembly of sequencing reads and the other for designing repeat-flanking primers for MS candidate loci, (iii) incorporate the widely used primer design program PRIMER 3 into STADEN workflows, enabling the interactive design and visualization of flanking primers for Microsatellites, and (iv) provide the functionality to find optimal locus- and primer pair combinations for multiplex primer design. Furthermore, our extensions include a module for storing analysis results in an SQLite database, providing a transparent solution for data access from within as well as from outside of the STADEN Package. The STADEN package is enhanced by our modules into a highly flexible, high-throughput, interactive tool for conventional and multiplex Microsatellite Marker design. It gives the user detailed control over the workflow, enabling flexible combinations of manual and automated analysis steps. The software is available under the OpenBSD License [1, 2]. The high efficiency of our automated Marker design workflow has been confirmed in three Microsatellite development projects.
Lars Kraemer - One of the best experts on this subject based on the ideXlab platform.
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STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive Microsatellite Marker design
BMC Bioinformatics, 2009Co-Authors: Lars Kraemer, Bánk Beszteri, Steffi Gäbler-schwarz, Christoph Held, Florian Leese, Christoph Mayer, Kevin Pöhlmann, Stephan FrickenhausAbstract:Background Microsatellites (MSs) are DNA Markers with high analytical power, which are widely used in population genetics, genetic mapping, and forensic studies. Currently available software solutions for high-throughput MS design (i) have shortcomings in detecting and distinguishing imperfect and perfect MSs, (ii) lack often necessary interactive design steps, and (iii) do not allow for the development of primers for multiplex amplifications. We present a set of new tools implemented as extensions to the S TADEN package, which provides the backbone functionality for flexible sequence analysis workflows. The possibility to assemble overlapping reads into unique contigs (provided by the base functionality of the S TADEN package) is important to avoid developing redundant Markers, a feature missing from most other similar tools. Results Our extensions to the S TADEN package provide the following functionality to facilitate Microsatellite (and also minisatellite) Marker design: The new modules (i) integrate the state-of-the-art tandem repeat detection and analysis software P HOBOS into workflows, (ii) provide two separate repeat detection steps – with different search criteria – one for masking repetitive regions during assembly of sequencing reads and the other for designing repeat-flanking primers for MS candidate loci, (iii) incorporate the widely used primer design program P RIMER 3 into S TADEN workflows, enabling the interactive design and visualization of flanking primers for Microsatellites, and (iv) provide the functionality to find optimal locus- and primer pair combinations for multiplex primer design. Furthermore, our extensions include a module for storing analysis results in an SQLite database, providing a transparent solution for data access from within as well as from outside of the S TADEN Package. Conclusion The S TADEN package is enhanced by our modules into a highly flexible, high-throughput, interactive tool for conventional and multiplex Microsatellite Marker design. It gives the user detailed control over the workflow, enabling flexible combinations of manual and automated analysis steps. The software is available under the OpenBSD License [ 1 , 2 ]. The high efficiency of our automated Marker design workflow has been confirmed in three Microsatellite development projects.
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stamp extensions to the staden sequence analysis package for high throughput interactive Microsatellite Marker design
BMC Bioinformatics, 2009Co-Authors: Lars Kraemer, Bánk Beszteri, Christoph Held, Florian Leese, Christoph Mayer, Kevin Pöhlmann, Steffi Gablerschwarz, Stephan FrickenhausAbstract:Microsatellites (MSs) are DNA Markers with high analytical power, which are widely used in population genetics, genetic mapping, and forensic studies. Currently available software solutions for high-throughput MS design (i) have shortcomings in detecting and distinguishing imperfect and perfect MSs, (ii) lack often necessary interactive design steps, and (iii) do not allow for the development of primers for multiplex amplifications. We present a set of new tools implemented as extensions to the STADEN package, which provides the backbone functionality for flexible sequence analysis workflows. The possibility to assemble overlapping reads into unique contigs (provided by the base functionality of the STADEN package) is important to avoid developing redundant Markers, a feature missing from most other similar tools. Our extensions to the STADEN package provide the following functionality to facilitate Microsatellite (and also minisatellite) Marker design: The new modules (i) integrate the state-of-the-art tandem repeat detection and analysis software PHOBOS into workflows, (ii) provide two separate repeat detection steps – with different search criteria – one for masking repetitive regions during assembly of sequencing reads and the other for designing repeat-flanking primers for MS candidate loci, (iii) incorporate the widely used primer design program PRIMER 3 into STADEN workflows, enabling the interactive design and visualization of flanking primers for Microsatellites, and (iv) provide the functionality to find optimal locus- and primer pair combinations for multiplex primer design. Furthermore, our extensions include a module for storing analysis results in an SQLite database, providing a transparent solution for data access from within as well as from outside of the STADEN Package. The STADEN package is enhanced by our modules into a highly flexible, high-throughput, interactive tool for conventional and multiplex Microsatellite Marker design. It gives the user detailed control over the workflow, enabling flexible combinations of manual and automated analysis steps. The software is available under the OpenBSD License [1, 2]. The high efficiency of our automated Marker design workflow has been confirmed in three Microsatellite development projects.
Matthew W Blair - One of the best experts on this subject based on the ideXlab platform.
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Microsatellite Marker diversity in common bean phaseolus vulgaris l
Theoretical and Applied Genetics, 2006Co-Authors: Matthew W Blair, Martha C Giraldo, Hector F Buendia, Eduardo Tovar, Myriam C Duque, Steve BeebeAbstract:A diversity survey was used to estimate allelic diversity and heterozygosity of 129 Microsatellite Markers in a panel of 44 common bean (Phaseolus vulgaris L.) genotypes that have been used as parents of mapping populations. Two types of Microsatellites were evaluated, based respectively on gene coding and genomic sequences. Genetic diversity was evaluated by estimating the polymorphism information content (PIC), as well as the distribution and range of alleles sizes. Gene-based Microsatellites proved to be less polymorphic than genomic Microsatellites in terms of both number of alleles (6.0 vs. 9.2) and PIC values (0.446 vs. 0.594) while greater size differences between the largest and the smallest allele were observed for the genomic Microsatellites than for the gene-based Microsatellites (31.4 vs. 19.1 bp). Markers that showed a high number of alleles were identified with a maximum of 28 alleles for the Marker BMd1. The Microsatellites were useful for distinguishing Andean and Mesoamerican genotypes, for uncovering the races within each genepool and for separating wild accessions from cultivars. Greater polymorphism and race structure was found within the Andean gene pool than within the Mesoamerican gene pool and polymorphism rate between genotypes was consistent with genepool and race identity. Comparisons between Andean genotypes had higher polymorphism (53.0%) on average than comparisons among Mesoamerican genotypes (33.4%). Within the Mesoamerican parental combinations, the intra-racial combinations between Mesoamerica and Durango or Jalisco race genotypes showed higher average rates of polymorphism (37.5%) than the within-race combinations between Mesoamerica race genotypes (31.7%). In multiple correspondance analysis we found two principal clusters of genotypes corresponding to the Mesoamerican and Andean gene pools and subgroups representing specific races especially for the Nueva Granada and Peru races of the Andean gene pool. Intra population diversity was higher within the Andean genepool than within the Mesoamerican genepool and this pattern was observed for both gene-based and genomic Microsatellites. Furthermore, intra-population diversity within the Andean races (0.356 on average) was higher than within the Mesoamerican races (0.302). Within the Andean gene pool, race Peru had higher diversity compared to race Nueva Granada, while within the Mesoamerican gene pool, the races Durango, Guatemala and Jalisco had comparable levels of diversity which were below that of race Mesoamerica.
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Microsatellite Marker development mapping and applications in rice genetics and breeding
Plant Molecular Biology, 1997Co-Authors: Susan R Mccouch, X Chen, Olivier Panaud, Svetlana V Temnykh, Yong Gu Cho, N Huang, Takashige Ishii, Matthew W BlairAbstract:Microsatellites are simple, tandemly repeated di- to tetra-nucleotide sequence motifs flanked by unique sequences. They are valuable as genetic Markers because they are co-dominant, detect high levels of allelic diversity, and are easily and economically assayed by the polymerase chain reaction (PCR). Results from screening a rice genomic library suggest that there are an estimated 5700-10 000 Microsatellites in rice, with the relative frequency of different repeats decreasing with increasing size of the motif. A map consisting of 120 Microsatellite Markers demonstrates that they are well distributed throughout the 12 chromosomes of rice. Five multiple copy primer sequences have been identified that could be mapped to independent chromosomal locations. The current level of genome coverage provided by these simple sequence length polymorphisms (SSLPs) in rice is sufficient to be useful for genotype identification, gene and quantitative trait locus (QTL) analysis, screening of large insert libraries, and Marker-assisted selection in breeding. Studies of allelic diversity have documented up to 25 alleles at a single locus in cultivated rice germplasm and provide evidence that amplification in wild relatives of Oryza sativa is generally reliable. The availability of increasing numbers of mapped SSLP Markers can be expected to complement existing RFLP and AFLP maps, increasing the power and resolution of genome analysis in rice.
Kevin Pöhlmann - One of the best experts on this subject based on the ideXlab platform.
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STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive Microsatellite Marker design
BMC Bioinformatics, 2009Co-Authors: Lars Kraemer, Bánk Beszteri, Steffi Gäbler-schwarz, Christoph Held, Florian Leese, Christoph Mayer, Kevin Pöhlmann, Stephan FrickenhausAbstract:Background Microsatellites (MSs) are DNA Markers with high analytical power, which are widely used in population genetics, genetic mapping, and forensic studies. Currently available software solutions for high-throughput MS design (i) have shortcomings in detecting and distinguishing imperfect and perfect MSs, (ii) lack often necessary interactive design steps, and (iii) do not allow for the development of primers for multiplex amplifications. We present a set of new tools implemented as extensions to the S TADEN package, which provides the backbone functionality for flexible sequence analysis workflows. The possibility to assemble overlapping reads into unique contigs (provided by the base functionality of the S TADEN package) is important to avoid developing redundant Markers, a feature missing from most other similar tools. Results Our extensions to the S TADEN package provide the following functionality to facilitate Microsatellite (and also minisatellite) Marker design: The new modules (i) integrate the state-of-the-art tandem repeat detection and analysis software P HOBOS into workflows, (ii) provide two separate repeat detection steps – with different search criteria – one for masking repetitive regions during assembly of sequencing reads and the other for designing repeat-flanking primers for MS candidate loci, (iii) incorporate the widely used primer design program P RIMER 3 into S TADEN workflows, enabling the interactive design and visualization of flanking primers for Microsatellites, and (iv) provide the functionality to find optimal locus- and primer pair combinations for multiplex primer design. Furthermore, our extensions include a module for storing analysis results in an SQLite database, providing a transparent solution for data access from within as well as from outside of the S TADEN Package. Conclusion The S TADEN package is enhanced by our modules into a highly flexible, high-throughput, interactive tool for conventional and multiplex Microsatellite Marker design. It gives the user detailed control over the workflow, enabling flexible combinations of manual and automated analysis steps. The software is available under the OpenBSD License [ 1 , 2 ]. The high efficiency of our automated Marker design workflow has been confirmed in three Microsatellite development projects.
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stamp extensions to the staden sequence analysis package for high throughput interactive Microsatellite Marker design
BMC Bioinformatics, 2009Co-Authors: Lars Kraemer, Bánk Beszteri, Christoph Held, Florian Leese, Christoph Mayer, Kevin Pöhlmann, Steffi Gablerschwarz, Stephan FrickenhausAbstract:Microsatellites (MSs) are DNA Markers with high analytical power, which are widely used in population genetics, genetic mapping, and forensic studies. Currently available software solutions for high-throughput MS design (i) have shortcomings in detecting and distinguishing imperfect and perfect MSs, (ii) lack often necessary interactive design steps, and (iii) do not allow for the development of primers for multiplex amplifications. We present a set of new tools implemented as extensions to the STADEN package, which provides the backbone functionality for flexible sequence analysis workflows. The possibility to assemble overlapping reads into unique contigs (provided by the base functionality of the STADEN package) is important to avoid developing redundant Markers, a feature missing from most other similar tools. Our extensions to the STADEN package provide the following functionality to facilitate Microsatellite (and also minisatellite) Marker design: The new modules (i) integrate the state-of-the-art tandem repeat detection and analysis software PHOBOS into workflows, (ii) provide two separate repeat detection steps – with different search criteria – one for masking repetitive regions during assembly of sequencing reads and the other for designing repeat-flanking primers for MS candidate loci, (iii) incorporate the widely used primer design program PRIMER 3 into STADEN workflows, enabling the interactive design and visualization of flanking primers for Microsatellites, and (iv) provide the functionality to find optimal locus- and primer pair combinations for multiplex primer design. Furthermore, our extensions include a module for storing analysis results in an SQLite database, providing a transparent solution for data access from within as well as from outside of the STADEN Package. The STADEN package is enhanced by our modules into a highly flexible, high-throughput, interactive tool for conventional and multiplex Microsatellite Marker design. It gives the user detailed control over the workflow, enabling flexible combinations of manual and automated analysis steps. The software is available under the OpenBSD License [1, 2]. The high efficiency of our automated Marker design workflow has been confirmed in three Microsatellite development projects.