Aptaligner: Automated Software for Aligning Pseudorandom DNA X-Aptamers from Next-Generation Sequencing Data

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• 作者：Emily Lu ; Miguel-Angel Elizondo-Riojas ; Jeffrey T. Chang ; David E. Volk
• 刊名：Biochemistry
• 出版年：2014
• 出版时间：June 10, 2014
• 年：2014
• 卷：53
• 期：22
• 页码：3523-3525
• 全文大小：194K
• 年卷期：v.53,no.22(June 10, 2014)
• ISSN：1520-4995

文摘

Next-generation sequencing results from bead-based aptamer libraries have demonstrated that traditional DNA/RNA alignment software is insufficient. This is particularly true for X-aptamers containing specialty bases (W, X, Y, Z, ...) that are identified by special encoding. Thus, we sought an automated program that uses the inherent design scheme of bead-based X-aptamers to create a hypothetical reference library and Markov modeling techniques to provide improved alignments. Aptaligner provides this feature as well as length error and noise level cutoff features, is parallelized to run on multiple central processing units (cores), and sorts sequences from a single chip into projects and subprojects.