使用TAGdb进行基因组区域的TAG序列鉴定。

TAG Sequence Identification of Genomic Regions Using TAGdb.

作者信息

Ruperao Pradeep

机构信息

School of Agriculture and Food Sciences, University of Queensland, Hartley Teakle Building 83, St. Lucia, QLD, 4072, Australia.

School of Plant Biology, University of Western Australia, Perth, WA, 6009, Australia.

出版信息

Methods Mol Biol. 2016;1374:233-40. doi: 10.1007/978-1-4939-3167-5_12.

DOI:10.1007/978-1-4939-3167-5_12

PMID:26519409

Abstract

Second-generation sequencing (SGS) technology has enabled the sequencing of genomes and identification of genes. However, large complex plant genomes remain particularly difficult for de novo assembly. Access to the vast quantity of raw sequence data may facilitate discoveries; however the volume of this data makes access difficult. This chapter discusses the Web-based tool TAGdb that enables researchers to identify paired read second-generation DNA sequence data that share identity with a submitted query sequence. The identified reads can be used for PCR amplification of genomic regions to identify genes and promoters without the need for genome assembly.

摘要

第二代测序（SGS）技术已实现基因组测序和基因鉴定。然而，大型复杂植物基因组的从头组装仍然特别困难。获取大量原始序列数据可能有助于发现；然而，这些数据的量使得访问变得困难。本章讨论了基于网络的工具TAGdb，它使研究人员能够识别与提交的查询序列具有相同身份的配对读取第二代DNA序列数据。所识别的读取可用于基因组区域的PCR扩增，以鉴定基因和启动子，而无需进行基因组组装。