Large Scale Explorative Oligonucleotide Probe Selection for Thousands of Genetic Groups on a Computing Grid: Application to Phylogenetic Probe Design Using a Curated Small Subunit Ribosomal RNA Gene Database
المؤلفون المشاركون
Jaziri, Faouzi
Peyretaillade, Eric
Missaoui, Mohieddine
Parisot, Nicolas
Cipière, Sébastien
Denonfoux, Jérémie
Mahul, Antoine
Hill, David R. C.
Peyret, Pierre
المصدر
العدد
المجلد 2014، العدد 2014 (31 ديسمبر/كانون الأول 2014)، ص ص. 1-9، 9ص.
الناشر
Hindawi Publishing Corporation
تاريخ النشر
2014-01-06
دولة النشر
مصر
عدد الصفحات
9
التخصصات الرئيسية
الطب البشري
تكنولوجيا المعلومات وعلم الحاسوب
الملخص EN
Phylogenetic Oligonucleotide Arrays (POAs) were recently adapted for studying the huge microbial communities in a flexible and easy-to-use way.
POA coupled with the use of explorative probes to detect the unknown part is now one of the most powerful approaches for a better understanding of microbial community functioning.
However, the selection of probes remains a very difficult task.
The rapid growth of environmental databases has led to an exponential increase of data to be managed for an efficient design.
Consequently, the use of high performance computing facilities is mandatory.
In this paper, we present an efficient parallelization method to select known and explorative oligonucleotide probes at large scale using computing grids.
We implemented a software that generates and monitors thousands of jobs over the European Computing Grid Infrastructure (EGI).
We also developed a new algorithm for the construction of a high-quality curated phylogenetic database to avoid erroneous design due to bad sequence affiliation.
We present here the performance and statistics of our method on real biological datasets based on a phylogenetic prokaryotic database at the genus level and a complete design of about 20,000 probes for 2,069 genera of prokaryotes.
نمط استشهاد جمعية علماء النفس الأمريكية (APA)
Jaziri, Faouzi& Peyretaillade, Eric& Missaoui, Mohieddine& Parisot, Nicolas& Cipière, Sébastien& Denonfoux, Jérémie…[et al.]. 2014. Large Scale Explorative Oligonucleotide Probe Selection for Thousands of Genetic Groups on a Computing Grid: Application to Phylogenetic Probe Design Using a Curated Small Subunit Ribosomal RNA Gene Database. The Scientific World Journal،Vol. 2014, no. 2014, pp.1-9.
https://search.emarefa.net/detail/BIM-1049290
نمط استشهاد الجمعية الأمريكية للغات الحديثة (MLA)
Jaziri, Faouzi…[et al.]. Large Scale Explorative Oligonucleotide Probe Selection for Thousands of Genetic Groups on a Computing Grid: Application to Phylogenetic Probe Design Using a Curated Small Subunit Ribosomal RNA Gene Database. The Scientific World Journal No. 2014 (2014), pp.1-9.
https://search.emarefa.net/detail/BIM-1049290
نمط استشهاد الجمعية الطبية الأمريكية (AMA)
Jaziri, Faouzi& Peyretaillade, Eric& Missaoui, Mohieddine& Parisot, Nicolas& Cipière, Sébastien& Denonfoux, Jérémie…[et al.]. Large Scale Explorative Oligonucleotide Probe Selection for Thousands of Genetic Groups on a Computing Grid: Application to Phylogenetic Probe Design Using a Curated Small Subunit Ribosomal RNA Gene Database. The Scientific World Journal. 2014. Vol. 2014, no. 2014, pp.1-9.
https://search.emarefa.net/detail/BIM-1049290
نوع البيانات
مقالات
لغة النص
الإنجليزية
الملاحظات
Includes bibliographical references
رقم السجل
BIM-1049290
قاعدة معامل التأثير والاستشهادات المرجعية العربي "ارسيف Arcif"
أضخم قاعدة بيانات عربية للاستشهادات المرجعية للمجلات العلمية المحكمة الصادرة في العالم العربي
تقوم هذه الخدمة بالتحقق من التشابه أو الانتحال في الأبحاث والمقالات العلمية والأطروحات الجامعية والكتب والأبحاث باللغة العربية، وتحديد درجة التشابه أو أصالة الأعمال البحثية وحماية ملكيتها الفكرية. تعرف اكثر