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CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites
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...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4829253/ https://www.ncbi.nlm.nih.gov/pubmed/27071032 http://dx.doi.org/10.1371/journal.pone.0152404 |
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author | Sharpe, Richard M. Koepke, Tyson Harper, Artemus Grimes, John Galli, Marco Satoh-Cruz, Mio Kalyanaraman, Ananth Evans, Katherine Kramer, David Dhingra, Amit |
author_facet | Sharpe, Richard M. Koepke, Tyson Harper, Artemus Grimes, John Galli, Marco Satoh-Cruz, Mio Kalyanaraman, Ananth Evans, Katherine Kramer, David Dhingra, Amit |
author_sort | Sharpe, Richard M. |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-4829253 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-48292532016-04-22 CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites Sharpe, Richard M. Koepke, Tyson Harper, Artemus Grimes, John Galli, Marco Satoh-Cruz, Mio Kalyanaraman, Ananth Evans, Katherine Kramer, David Dhingra, Amit PLoS One Research Article 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. Public Library of Science 2016-04-12 /pmc/articles/PMC4829253/ /pubmed/27071032 http://dx.doi.org/10.1371/journal.pone.0152404 Text en © 2016 Sharpe et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Sharpe, Richard M. Koepke, Tyson Harper, Artemus Grimes, John Galli, Marco Satoh-Cruz, Mio Kalyanaraman, Ananth Evans, Katherine Kramer, David Dhingra, Amit CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites |
title | CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites |
title_full | CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites |
title_fullStr | CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites |
title_full_unstemmed | CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites |
title_short | CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites |
title_sort | cissers: customizable in silico sequence evaluation for restriction sites |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4829253/ https://www.ncbi.nlm.nih.gov/pubmed/27071032 http://dx.doi.org/10.1371/journal.pone.0152404 |
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