EasyDIVER: A Pipeline for Assembling and Counting High-Throughput Sequencing Data from In Vitro Evolution of Nucleic Acids or Peptides

Blanco Celia; Verbanic Samuel; Seelig Burckhard; Chen Irene A.

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EasyDIVER: A Pipeline for Assembling and Counting High-Throughput Sequencing Data from In Vitro Evolution of Nucleic Acids or Peptides

机译：EasyDiver：用于组装和计数来自核酸或肽的体外演变的高通量测序数据的管道

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摘要

In vitro evolution is a well-established technique for the discovery of functional RNA and peptides. Increasingly, these experiments are analyzed by high-throughput sequencing (HTS) for both scientific and engineering objectives, but computational analysis of HTS data, particularly for peptide selections, can present a barrier to entry for experimentalists. We introduce EasyDIVER (Easypre-processing andDereplication ofInVitroEvolutionReads), a simple, user-friendly pipeline for processing high-throughput sequencing data from in vitro selections and directed evolution experiments. The pipeline takes as input raw, paired-end, demultiplexed Illumina read files. For each sample provided, EasyDIVER outputs a dereplicated list of unique nucleic acid and/or peptide sequences and their count reads.

机译：体外进化是用于发现功能性RNA和肽的良好技术。这些实验越来越多地通过高通量测序（HTS）来分析科学和工程目标，但HTS数据的计算分析，特别是对于肽选择，可以为实验主义者提供障碍。我们介绍EasyDiver（EasyPre-Procession AndForovolutionReads），简单，用户友好的管道，用于处理来自体外选择和定向演化实验的高通量测序数据。管道作为输入原始，配对端，解复用的illumina读取文件。对于所提供的每个样本，EasyDiver输出独特的核酸和/或肽序列的无所作为的列表及其计数读数。

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来源
《Journal of Molecular Evolution》 |2020年第6期|共5页
作者
Blanco Celia; Verbanic Samuel; Seelig Burckhard; Chen Irene A.;
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作者单位

Univ Calif Santa Barbara Dept Chem &

Biochem 9510 Santa Barbara CA 93106 USA;

Univ Calif Los Angeles Dept Chem &

Biomol Engn Los Angeles CA 90095 USA;

Univ Minnesota Dept Biochem Mol Biol &

Biophys Minneapolis MN 55455 USA;

Univ Calif Santa Barbara Dept Chem &

Biochem 9510 Santa Barbara CA 93106 USA;

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原文格式 PDF
正文语种 eng
中图分类进化论、生物系统发育;
关键词
High-throughput sequencing; mRNA display; In vitro evolution; SELEX; Bioinformatics;

机译：高通量测序;mRNA显示;体外进化;SELEX;生物信息学;

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专利

1. EasyDIVER: A Pipeline for Assembling and Counting High-Throughput Sequencing Data from In Vitro Evolution of Nucleic Acids or Peptides [J] . Blanco Celia, Verbanic Samuel, Seelig Burckhard, Journal of Molecular Evolution . 2020,第6期

机译：EasyDiver：用于组装和计数来自核酸或肽的体外演变的高通量测序数据的管道
2. Differential effects on the miRNome of the treatment of human airway epithelial Calu-3 cells with peptide-nucleic acids (PNAs) targeting microRNAs miR-101-3p and miR-145-5p: Next generation sequencing datasets [J] . Jessica Gasparello, Enrica Fabbri, Roberto Gambari, Data in Brief . 2021,第3期

机译：用肽 - 核酸（PNAS）靶向MicroRNAS miR-101-3P和MIR-145-5P的靶向核酸治疗人体气道上皮钙钙细胞的微分作用：下一代测序数据集
3. Self-assembling asymmetric peptide-dendrimer micelles – a platform for effective and versatile in vitro nucleic acid delivery [J] . Ganesh R. Kokil, Rakesh N. Veedu, Bao Tri Le, Scientific reports. . 2018,第1期

机译：自组装不对称肽树状聚合物胶束–有效和通用的体外核酸递送平台
4. Enzymatic ligation of peptides, peptide nucleic acids and proteins by means of sortase A [C] . Stephan Pritz, Yvonne Wolf, Oliver Kraetke American Peptide Symposium . 2009

机译：肽，肽核酸和蛋白质通过分子A的酶促结扎
5. Development of in vitro selection strategies for generating new catalytic nucleic acids and peptides. [D] . Pobanz, Kelsey. 2015

机译：开发用于产生新的催化核酸和肽的体外选择策略。
6. EasyDIVER: A Pipeline for Assembling and Counting High-Throughput Sequencing Data from In Vitro Evolution of Nucleic Acids or Peptides [O] . Celia Blanco, Samuel Verbanic, Burckhard Seelig, -1

机译：EasyDIVER：一种用于从核酸或肽的体外进化中组装和计算高通量测序数据的管道
7. EasyDIVER: A Pipeline for Assembling and Counting High-Throughput Sequencing Data from In Vitro Evolution of Nucleic Acids or Peptides [O] . Celia Blanco, Samuel Verbanic, Burckhard Seelig, 2020

机译：EasyDiver：一种用于组装和计数来自核酸或肽的体外演变的高通量测序数据的管道
8. In Vitro Assessment of a Peptide Nucleic Acid (PNA) - Peptide Conjugate Labeled With an Auger-Emitting Radionuclide for Prostate Cell Killing [R] . Wilbur, S. D. 2005

机译：体外评估肽核酸（pNa） - 用俄歇发射放射性核素标记的肽缀合物用于前列腺细胞杀伤

EasyDIVER: A Pipeline for Assembling and Counting High-Throughput Sequencing Data from In Vitro Evolution of Nucleic Acids or Peptides

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