期刊
MOLECULAR THERAPY-NUCLEIC ACIDS
卷 4, 期 -, 页码 -出版社
CELL PRESS
DOI: 10.1038/mtna.2015.4
关键词
aptamer; bioinformatics; high-throughput sequence; next-generation sequencing; phage display; ribozyme; sequencing; SELEX; software
资金
- National Science Foundation Chemistry of Life Processes award [CHE-1057506]
- National Aeronautics and Space Administration Exobiology award [NAG5-12360]
High-throughput sequence (HTS) analysis of combinatorial selection populations accelerates lead discovery and optimization and offers dynamic insight into selection processes. An underlying principle is that selection enriches high-fitness sequences as a fraction of the population, whereas low-fitness sequences are depleted. HTS analysis readily provides the requisite numerical information by tracking the evolutionary trajectory of individual sequences in response to selection pressures. Unlike genomic data, for which a number of software solutions exist, user-friendly tools are not readily available for the combinatorial selections field, leading many users to create custom software. FASTAptamer was designed to address the sequence-level analysis needs of the field. The open source FASTAptamer toolkit counts, normalizes and ranks read counts in a FASTQ file, compares populations for sequence distribution, generates clusters of sequence families, calculates fold-enrichment of sequences throughout the course of a selection and searches for degenerate sequence motifs. While originally designed for aptamer selections, FASTAptamer can be applied to any selection strategy that can utilize next-generation DNA sequencing, such as ribozyme or deoxyribozyme selections, in vivo mutagenesis and various surface display technologies (peptide, antibody fragment, mRNA, etc.).
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