CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites
Abstract
High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Here, 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 CisSERSenable 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 ofmore »
- Authors:
- Publication Date:
- Research Org.:
- Washington State Univ., Pullman, WA (United States); Michigan State Univ., East Lansing, MI (United States). MSU-DOE Plant Research Laboratory
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH); Washington State University (WSU)
- OSTI Identifier:
- 1346599
- Alternate Identifier(s):
- OSTI ID: 1257836
- Grant/Contract Number:
- FG02-04ER15559; FG02-91ER20021; 2008 -35300-04676; T32GM008336; IOS 0641232; MCB 1146928
- Resource Type:
- Published Article
- Journal Name:
- PLoS ONE
- Additional Journal Information:
- Journal Name: PLoS ONE Journal Volume: 11 Journal Issue: 4; Journal ID: ISSN 1932-6203
- Publisher:
- Public Library of Science
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; sequence motif analysis; DNA sequence analysis; sequence analysis; arabidopsis thaliana; expressed sequence tags; sequence databases; plant genomics; genome analysis
Citation Formats
Sharpe, Richard M., Koepke, Tyson, Harper, Artemus, Grimes, John, Galli, Marco, Satoh-Cruz, Mio, Kalyanaraman, Ananth, Evans, Katherine, Kramer, David, Dhingra, Amit, and Prasad, ed., Manoj. CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites. United States: N. p., 2016.
Web. doi:10.1371/journal.pone.0152404.
Sharpe, Richard M., Koepke, Tyson, Harper, Artemus, Grimes, John, Galli, Marco, Satoh-Cruz, Mio, Kalyanaraman, Ananth, Evans, Katherine, Kramer, David, Dhingra, Amit, & Prasad, ed., Manoj. CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites. United States. https://doi.org/10.1371/journal.pone.0152404
Sharpe, Richard M., Koepke, Tyson, Harper, Artemus, Grimes, John, Galli, Marco, Satoh-Cruz, Mio, Kalyanaraman, Ananth, Evans, Katherine, Kramer, David, Dhingra, Amit, and Prasad, ed., Manoj. Tue .
"CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites". United States. https://doi.org/10.1371/journal.pone.0152404.
@article{osti_1346599,
title = {CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites},
author = {Sharpe, Richard M. and Koepke, Tyson and Harper, Artemus and Grimes, John and Galli, Marco and Satoh-Cruz, Mio and Kalyanaraman, Ananth and Evans, Katherine and Kramer, David and Dhingra, Amit and Prasad, ed., Manoj},
abstractNote = {High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Here, 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 CisSERSenable 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 CisSERSand 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.},
doi = {10.1371/journal.pone.0152404},
journal = {PLoS ONE},
number = 4,
volume = 11,
place = {United States},
year = {Tue Apr 12 00:00:00 EDT 2016},
month = {Tue Apr 12 00:00:00 EDT 2016}
}
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https://doi.org/10.1371/journal.pone.0152404
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Works referenced in this record:
Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library
journal, January 2009
- Sánchez, Cecilia; Smith, Timothy PL; Wiedmann, Ralph T.
- BMC Genomics, Vol. 10, Issue 1
SNP Cutter: a comprehensive tool for SNP PCR-RFLP assay design
journal, July 2005
- Zhang, R.; Zhu, Z.; Zhu, H.
- Nucleic Acids Research, Vol. 33, Issue Web Server
Web-based primer design for single nucleotide polymorphism analysis
journal, December 2002
- Neff, Michael M.; Turk, Edward; Kalishman, Michael
- Trends in Genetics, Vol. 18, Issue 12
Single-reaction for SNP Genotyping on Agarose Gel by Allele-specific PCR in Black Poplar (Populus nigra L.)
journal, June 2007
- Gaudet, Muriel; Fara, Anna-Giulia; Sabatti, Maurizio
- Plant Molecular Biology Reporter, Vol. 25, Issue 1-2
Advances in molecular marker techniques and their applications in plant sciences
journal, February 2008
- Agarwal, Milee; Shrivastava, Neeta; Padh, Harish
- Plant Cell Reports, Vol. 27, Issue 4
Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley
journal, January 2011
- Chutimanitsakun, Yada; Nipper, Rick W.; Cuesta-Marcos, Alfonso
- BMC Genomics, Vol. 12, Issue 1
CapsID: a web-based tool for developing parsimonious sets of CAPS molecular markers for genotyping
journal, May 2006
- Taylor, Jonathan; Provart, Nicholas J.
- BMC Genetics, Vol. 7, Issue 1
BlastDigester – a web-based program for efficient CAPS marker design
journal, July 2004
- Ilic, Katica; Berleth, Thomas; Provart, Nicholas J.
- Trends in Genetics, Vol. 20, Issue 7
SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries
journal, February 2008
- Van Tassell, Curtis P.; Smith, Timothy P. L.; Matukumalli, Lakshmi K.
- Nature Methods, Vol. 5, Issue 3
Rapid gene-based SNP and haplotype marker development in non-model eukaryotes using 3'UTR sequencing
journal, January 2012
- Koepke, Tyson; Schaeffer, Scott; Krishnan, Vandhana
- BMC Genomics, Vol. 13, Issue 1
The genome of the domesticated apple (Malus × domestica Borkh.)
journal, August 2010
- Velasco, Riccardo; Zharkikh, Andrey; Affourtit, Jason
- Nature Genetics, Vol. 42, Issue 10
SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping
journal, January 2010
- Chang, Hsueh-Wei; Cheng, Yu-Huei; Chuang, Li-Yeh
- BMC Bioinformatics, Vol. 11, Issue 1
NEBcutter: a program to cleave DNA with restriction enzymes
journal, July 2003
- Vincze, T.
- Nucleic Acids Research, Vol. 31, Issue 13
Transcript Profiling by 3′-Untranslated Region Sequencing Resolves Expression of Gene Families
journal, November 2007
- Eveland, Andrea L.; McCarty, Donald R.; Koch, Karen E.
- Plant Physiology, Vol. 146, Issue 1
SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development
journal, January 2004
- Thiel, T.
- Nucleic Acids Research, Vol. 32, Issue 1
Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers
journal, October 2008
- Baird, Nathan A.; Etter, Paul D.; Atwood, Tressa S.
- PLoS ONE, Vol. 3, Issue 10
SNPs discovery and CAPS marker conversion in soybean
journal, September 2010
- Shu, Yongjun; Li, Yong; Zhu, Zhenlei
- Molecular Biology Reports, Vol. 38, Issue 3