Journal article
CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites
PloS one, Vol.11(4), pp.e0152404-e0152404
2016
Handle:
https://hdl.handle.net/2376/109647
PMCID: PMC4829253
PMID: 27071032
Abstract
High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. CisSERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated to enhance the usefulness of the software. CisSERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, CisSERS utilizes the REBASE enzyme database. Results from CisSERS enable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3'UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. CisSERS is a java based graphical user interface built around a perl backbone. Several of the applications of CisSERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool CisSERS and results from in-silico and corresponding wet-lab analyses demonstrating that CisSERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies.
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Details
- Title
- CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites
- Creators
- Richard M Sharpe - School of Biological Sciences, Washington State University, Pullman, WA, Washington, United States of AmericaTyson Koepke - Department of Horticulture, Washington State University, Pullman, Washington, United States of AmericaArtemus Harper - Department of Horticulture, Washington State University, Pullman, Washington, United States of AmericaJohn Grimes - Electrical Engineering and Computer Science, Washington State University, Pullman, Washington, United States of AmericaMarco Galli - Department of Horticulture, Washington State University, Pullman, Washington, United States of AmericaMio Satoh-Cruz - MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, United States of AmericaAnanth Kalyanaraman - Electrical Engineering and Computer Science, Washington State University, Pullman, Washington, United States of AmericaKatherine Evans - Department of Horticulture, Washington State University, Pullman, Washington, United States of AmericaDavid Kramer - MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, United States of AmericaAmit Dhingra - Department of Horticulture, Washington State University, Pullman, Washington, United States of America
- Publication Details
- PloS one, Vol.11(4), pp.e0152404-e0152404
- Academic Unit
- WSU Wenatchee Tree Fruit REC; Crop and Soil Sciences, Department of; Horticulture, Department of; Electrical Engineering and Computer Science, School of
- Publisher
- United States
- Grant note
- T32 GM008336 / NIGMS NIH HHS T32GM008336 / NIGMS NIH HHS
- Identifiers
- 99900547490901842
- Language
- English
- Resource Type
- Journal article