Error Analysis of Deep Sequencing of Phage Libraries : Peptides Censored in Sequencing
المؤلفون المشاركون
Matochko, Wadim L.
Derda, Ratmir
المصدر
Computational and Mathematical Methods in Medicine
العدد
المجلد 2013، العدد 2013 (31 ديسمبر/كانون الأول 2013)، ص ص. 1-13، 13ص.
الناشر
Hindawi Publishing Corporation
تاريخ النشر
2013-12-12
دولة النشر
مصر
عدد الصفحات
13
التخصصات الرئيسية
الملخص EN
Next-generation sequencing techniques empower selection of ligands from phage-display libraries because they can detect low abundant clones and quantify changes in the copy numbers of clones without excessive selection rounds.
Identification of errors in deep sequencing data is the most critical step in this process because these techniques have error rates >1%.
Mechanisms that yield errors in Illumina and other techniques have been proposed, but no reports to date describe error analysis in phage libraries.
Our paper focuses on error analysis of 7-mer peptide libraries sequenced by Illumina method.
Low theoretical complexity of this phage library, as compared to complexity of long genetic reads and genomes, allowed us to describe this library using convenient linear vector and operator framework.
We describe a phage library as N×1 frequency vector n=ni, where ni is the copy number of the ith sequence and N is the theoretical diversity, that is, the total number of all possible sequences.
Any manipulation to the library is an operator acting on n.
Selection, amplification, or sequencing could be described as a product of a N×N matrix and a stochastic sampling operator (Sa).
The latter is a random diagonal matrix that describes sampling of a library.
In this paper, we focus on the properties of Sa and use them to define the sequencing operator (Seq).
Sequencing without any bias and errors is Seq=Sa IN, where IN is a N×N unity matrix.
Any bias in sequencing changes IN to a nonunity matrix.
We identified a diagonal censorship matrix (CEN), which describes elimination or statistically significant downsampling, of specific reads during the sequencing process.
نمط استشهاد جمعية علماء النفس الأمريكية (APA)
Matochko, Wadim L.& Derda, Ratmir. 2013. Error Analysis of Deep Sequencing of Phage Libraries : Peptides Censored in Sequencing. Computational and Mathematical Methods in Medicine،Vol. 2013, no. 2013, pp.1-13.
https://search.emarefa.net/detail/BIM-475872
نمط استشهاد الجمعية الأمريكية للغات الحديثة (MLA)
Matochko, Wadim L.& Derda, Ratmir. Error Analysis of Deep Sequencing of Phage Libraries : Peptides Censored in Sequencing. Computational and Mathematical Methods in Medicine No. 2013 (2013), pp.1-13.
https://search.emarefa.net/detail/BIM-475872
نمط استشهاد الجمعية الطبية الأمريكية (AMA)
Matochko, Wadim L.& Derda, Ratmir. Error Analysis of Deep Sequencing of Phage Libraries : Peptides Censored in Sequencing. Computational and Mathematical Methods in Medicine. 2013. Vol. 2013, no. 2013, pp.1-13.
https://search.emarefa.net/detail/BIM-475872
نوع البيانات
مقالات
لغة النص
الإنجليزية
الملاحظات
Includes bibliographical references
رقم السجل
BIM-475872
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