Natwest T20 Blast Score Estimation Using Vectors and Modulus Operation

2016 ◽  
Author(s):  
Prasant Nair
Keyword(s):  
Blast Score

scholarly journals The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes

2014 ◽  
Author(s):  
Jason W Sahl ◽  
Greg Caporaso ◽  
David A Rasko ◽  
Paul S Keim
Keyword(s):  
Large Scale ◽  
Sequence Data ◽  
Parallel Implementation ◽  
Genetic Relationships ◽  
Clinical Diagnostics ◽  
Whole Genome Sequence ◽  
Bacterial Isolates ◽  
Bacterial Genomes ◽  
E Coli ◽  
Blast Score

Background. As whole genome sequence data from bacterial isolates becomes cheaper to generate, computational methods are needed to correlate sequence data with biological observations. Here we present the large-scale BLAST score ratio (LS-BSR) pipeline, which rapidly compares the genetic content of hundreds to thousands of bacterial genomes, and returns a matrix that describes the relatedness of all coding sequences (CDSs) in all genomes surveyed. This matrix can be easily parsed in order to identify genetic relationships between bacterial genomes. Although pipelines have been published that group peptides by sequence similarity, no other software performs the large-scale, flexible, full-genome comparative analyses carried out by LS-BSR. Results. To demonstrate the utility of the method, the LS-BSR pipeline was tested on 96 Escherichia coli and Shigella genomes; the pipeline ran in 163 minutes using 16 processors, which is a greater than 7-fold speedup compared to using a single processor. The BSR values for each CDS, which indicate a relative level of relatedness, were then mapped to each genome on an independent core genome single nucleotide polymorphism (SNP) based phylogeny. Comparisons were then used to identify clade specific CDS markers and validate the LS-BSR pipeline based on molecular markers that delineate between classical E. coli pathogenic variant (pathovar) designations. Scalability tests demonstrated that the LS-BSR pipeline can process 1,000 E. coli genomes in ~60h using 16 processors. Conclusions. LS-BSR is an open-source, parallel implementation of the BSR algorithm, enabling rapid comparison of the genetic content of large numbers of genomes. The results of the pipeline can be used to identify specific markers between user-defined phylogenetic groups, and to identify the loss and/or acquisition of genetic information between bacterial isolates. Taxa-specific genetic markers can then be translated into clinical diagnostics, or can be used to identify broadly conserved putative therapeutic candidates.

scholarly journals The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes

2014 ◽  
Author(s):  
Jason W Sahl ◽  
Greg Caporaso ◽  
David A Rasko ◽  
Paul S Keim
Keyword(s):  
Large Scale ◽  
Sequence Data ◽  
Parallel Implementation ◽  
Genetic Relationships ◽  
Clinical Diagnostics ◽  
Whole Genome Sequence ◽  
Bacterial Isolates ◽  
Bacterial Genomes ◽  
E Coli ◽  
Blast Score

Background. As whole genome sequence data from bacterial isolates becomes cheaper to generate, computational methods are needed to correlate sequence data with biological observations. Here we present the large-scale BLAST score ratio (LS-BSR) pipeline, which rapidly compares the genetic content of hundreds to thousands of bacterial genomes, and returns a matrix that describes the relatedness of all coding sequences (CDSs) in all genomes surveyed. This matrix can be easily parsed in order to identify genetic relationships between bacterial genomes. Although pipelines have been published that group peptides by sequence similarity, no other software performs the large-scale, flexible, full-genome comparative analyses carried out by LS-BSR. Results. To demonstrate the utility of the method, the LS-BSR pipeline was tested on 96 Escherichia coli and Shigella genomes; the pipeline ran in 163 minutes using 16 processors, which is a greater than 7-fold speedup compared to using a single processor. The BSR values for each CDS, which indicate a relative level of relatedness, were then mapped to each genome on an independent core genome single nucleotide polymorphism (SNP) based phylogeny. Comparisons were then used to identify clade specific CDS markers and validate the LS-BSR pipeline based on molecular markers that delineate between classical E. coli pathogenic variant (pathovar) designations. Scalability tests demonstrated that the LS-BSR pipeline can process 1,000 E. coli genomes in ~60h using 16 processors. Conclusions. LS-BSR is an open-source, parallel implementation of the BSR algorithm, enabling rapid comparison of the genetic content of large numbers of genomes. The results of the pipeline can be used to identify specific markers between user-defined phylogenetic groups, and to identify the loss and/or acquisition of genetic information between bacterial isolates. Taxa-specific genetic markers can then be translated into clinical diagnostics, or can be used to identify broadly conserved putative therapeutic candidates.

scholarly journals The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes

PeerJ ◽  
2014 ◽  
Vol 2 ◽  
pp. e332 ◽  
Author(s):  
Jason W. Sahl ◽  
J. Gregory Caporaso ◽  
David A. Rasko ◽  
Paul Keim
Keyword(s):  
Large Scale ◽  
Bacterial Genomes ◽  
Blast Score

scholarly journals Tapping Pennisetum violaceum, a Wild Relative of Pearl Millet (Pennisetum glaucum), for Resistance to Blast (caused by Magnaporthe grisea) and Rust (caused by Puccinia substriata var. indica)

Plant Disease ◽  
2020 ◽  
Vol 104 (5) ◽  
pp. 1487-1491 ◽  
Author(s):  
Rajan Sharma ◽  
Shivali Sharma ◽  
Vishal L. Gate
Keyword(s):  
Pearl Millet ◽  
Rust Resistance ◽  
Magnaporthe Grisea ◽  
Pennisetum Glaucum ◽  
Wild Relative ◽  
Blast Score ◽  
Genetic Stocks ◽  
Pedigree Selection ◽  
Rust Severity ◽  
The Mean

Blast (Magnaporthe grisea) and rust (Puccinia substriata var. indica) are the two important foliar diseases of pearl millet (Pennisetum glaucum (L.) R. Br.) that can be best managed through host plant resistance. For identification of diverse sources of blast and rust resistance, 305 accessions of Pennisetum violaceum, a wild relative of pearl millet, were screened under greenhouse conditions against five pathotype-isolates of M. grisea and a local isolate of P. substriata var. indica collected from ICRISAT farm, Patancheru, India. Based on the mean blast score (1 to 9 scale), 17 accessions (IP 21525, 21531, 21536, 21540, 21594, 21610, 21640, 21706, 21711, 21716, 21719, 21720, 21721, 21724, 21987, 21988, and 22160) were found resistant (score ≤3.0) to all five pathotypes, and 24 accessions were resistant to four pathotypes of M. grisea. As there was variability for rust resistance within some accessions, individual rust-resistant (<5% severity) plants from 17 accessions were selected, grown in pots and advanced to next generation by selfing, and rescreened for three to four generations following pedigree selection to develop rust-resistant genetic stocks. Single plant selections from nine accessions (IP 21629, 21645, 21658, 21660, 21662, 21711, 21974, 21975, and 22038) were found highly resistant to rust (0% rust severity) after four generations of pedigree selection and subsequent screening. Some of the blast-resistant accessions and rust-resistant genetic stocks are being utilized in a prebreeding program at ICRISAT for introgressing resistance genes from the wild into the parental lines of cultivated and potential pearl millet hybrids and varieties.

scholarly journals Seleksi Galur Mutan Padi Fatmawati Tahan terhadap Penyakit Blas dan Evaluasi Karakter Agronomi di Rumah Kaca dan di Lahan Sawah

2016 ◽  
Vol 21 (2) ◽  
pp. 79
Author(s):  
Endang G. Lestari ◽  
Iswari S. Dewi ◽  
Rossa Yunita
Keyword(s):  
Rice Variety ◽  
Blast Disease ◽  
Yield Potential ◽  
Agronomic Characters ◽  
Plant Type ◽  
Rice Varieties ◽  
Green House ◽  
Blast Score ◽  
Mutant Lines ◽  
Moderately Resistant

<p>Fatmawati, a rice variety released in 2003, is a new plant type (NPT) of rice that had different characteristic from existing high yielding rice varieties (HYV). The yield potential of this rice variety is 7.5 t/ha. Therefore its cultivated is expected to increase national rice production. However, the dissemination of this variety was hampered in several regions due to its susceptibility to blast disease and high percentage of empty grain caused by partially exserted and enclosed panicle. This research was conducted to evaluate 104 dihaploid mutant lines of Fatmawati for resistance to blast disease and good agronomic characters, especially for panicle exsertion rate. The first research was conducted in the endemic area of blast disease at Cikembar-Sukabumi, West Java. The blast disease resistance lines were then subsequently evaluated for their agronomic characters by planting in the green house and in the field. The results indicated that 40 dihaploid mutant lines were characterized as resistant and moderately resistant to blast (score 3&amp;ndash;5). Agronomic characters evaluation in the green house and in the field resulted in 11 dihaploid mutant lines with well exerted panicle (0% of coverage of panicle by flagleaf sheath) and high grains per panicle (229&amp;ndash;283 grains/panicle). Those lines were F99, F102, F116, F122, F130, F134, F138, F147, F149, F150, and F153.</p><p> </p><p><strong>Abstrak</strong></p><p>Fatmawati, varietas padi yang dilepas tahun 2003, adalah padi tipe baru (PTB) yang mempunyai karakteristik berbeda dari varietas padi unggul baru (VUB). Potensi hasil varietas padi ini adalah 7,5 t/ha. Penanaman varietas ini diharapkan akan meningkatkan produksi padi nasional. Namun, diseminasi varietas ini di beberapa tempat mengalami hambatan karena kerentanannya terhadap penyakit blas dan tingginya persentase gabah hampa akibat setengah tertutupnya atau tertutup semuanya malai oleh pelepah daun bendera. Penelitian ini dilakukan untuk mengevaluasi 104 galur mutan dihaploid turunan Fatmawati terhadap ketahanan blas dan karakter agronomi, khususnya laju keluarnya malai. Penelitian pertama dilakukan di daerah endemik penyakit blas di Cikembar- Sukabumi, Jawa Barat. Galur-galur yang tahan blas kemudian dievaluasi karakter agronominya dengan menanam di rumah kaca dan lapang. Hasil penelitian menunjukkan terdapat 40 galur mutan dihaploid dikategorikan sebagai tahan dan agak tahan penyakit blas (skor 3&amp;ndash;5). Evaluasi karakter agronomi di rumah kaca dan lapang menghasilkan 11 galur mutan dihaploid yang malainya sempurna keluar (0% penutupan malai oleh pelepah daun bendera) dan jumlah gabah/malai tinggi (229&amp;ndash;283 gabah/malai). Galur mutan dihaploid tersebut adalah galur F99, F102, F116, F122, F130, F134, F138, F147, F149, F150, dan F153.</p>

scholarly journals Identification of Blast Resistance in a Core Collection of Foxtail Millet Germplasm

Plant Disease ◽  
2014 ◽  
Vol 98 (4) ◽  
pp. 519-524 ◽  
Author(s):  
Rajan Sharma ◽  
A. G. Girish ◽  
H. D. Upadhyaya ◽  
P. Humayun ◽  
T. K. Babu ◽  
...  
Keyword(s):  
Core Collection ◽  
Magnaporthe Grisea ◽  
Blast Resistance ◽  
Foxtail Millet ◽  
Leaf Sheath ◽  
Leaf Blast ◽  
Blast Score ◽  
Serious Disease ◽  
Seedling Leaf ◽  
Yield Trials

Blast, also known as leaf spot, caused by Pyricularia grisea (teleomorph: Magnaporthe grisea), is a serious disease affecting both forage and grain production in foxtail millet in India. For the identification of new and diverse sources of blast resistance, a foxtail millet core collection comprising 155 accessions was evaluated against the Patancheru isolate (Fx 57) of M. grisea. In a field screen during 2009 and 2010, 21 accessions were identified with neck and head blast resistance against Fx 57. In a greenhouse screen, 11 of the 155 accessions exhibited seedling leaf blast resistance to the same isolate. Further evaluation of the selected 28 accessions (found resistant to neck and head blast under field conditions during 2009 and 2010 or leaf blast in the greenhouse screen) against four M. grisea isolates (Fx 57, Fx 58, Fx 60, and Fx 62 from Patancheru, Nandyal, Vizianagaram, and Mandya, respectively) led to the identification of 16 accessions with leaf, sheath, neck, and head blast resistance to at least one isolate. Two accessions (ISe 1181 and ISe 1547) were free from head blast infection and showed resistance to leaf (score ≤3.0 on a 1-to-9 scale), neck, and sheath blast (score ≤2.0 on a 1-to-5 scale) against all four isolates. In addition, ISe 1067 and ISe 1575 also exhibited high levels of blast resistance. Blast-resistant accessions with superior agronomic and nutritional quality traits can be evaluated in multilocation yield trials before releasing them for cultivation to farmers.

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