Abstract
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 (Easy pre-processing and Dereplication of In Vitro Evolution Reads), 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.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 477-481 |
| Number of pages | 5 |
| Journal | Journal of Molecular Evolution |
| Volume | 88 |
| Issue number | 6 |
| DOIs | |
| State | Published - Aug 1 2020 |
Bibliographical note
Funding Information:This work was supported by the Otis Williams Fund; the Simons Collaboration on the Origins of Life [Grant Number 340762 to B.S., 290356FY18 to I.C]; the US National Aeronautics and Space Administration [Grant Number NNX14AK29G to B.S., NNX16AJ32G to I.C.]; the NIH [GM108703 to B.S.]; and the NIH New Innovator Program [Grant Number DP2GM123457 to I.C.].
Keywords
- Bioinformatics
- High-throughput sequencing
- In vitro evolution
- SELEX
- mRNA display
PubMed: MeSH publication types
- Letter