cPlot: Contig-Plotting Visualization for the Analysis of Short-Read Nucleotide Sequence Alignments
Advances in the next-generation sequencing technology have led to a dramatic decrease in read-generation cost and an increase in read output. Reconstruction of short DNA sequence reads generated by next-generation sequencing requires a read alignment method that reconstructs a reference genome. In a...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-09-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/19/11484 |
| _version_ | 1797479071325618176 |
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| author | Mingeun Ji Yejin Kan Dongyeon Kim Jaehee Jung Gangman Yi |
| author_facet | Mingeun Ji Yejin Kan Dongyeon Kim Jaehee Jung Gangman Yi |
| author_sort | Mingeun Ji |
| collection | DOAJ |
| description | Advances in the next-generation sequencing technology have led to a dramatic decrease in read-generation cost and an increase in read output. Reconstruction of short DNA sequence reads generated by next-generation sequencing requires a read alignment method that reconstructs a reference genome. In addition, it is essential to analyze the results of read alignments for a biologically meaningful inference. However, read alignment from vast amounts of genomic data from various organisms is challenging in that it involves repeated automatic and manual analysis steps. We, here, devised cPlot software for read alignment of nucleotide sequences, with automated read alignment and position analysis, which allows visual assessment of the analysis results by the user. cPlot compares sequence similarity of reads by performing multiple read alignments, with FASTA format files as the input. This application provides a web-based interface for the user for facile implementation, without the need for a dedicated computing environment. cPlot identifies the location and order of the sequencing reads by comparing the sequence to a genetically close reference sequence in a way that is effective for visualizing the assembly of short reads generated by NGS and rapid gene map construction. |
| first_indexed | 2024-03-09T21:40:35Z |
| format | Article |
| id | doaj.art-cbd4af3e9a7144f0b5e851369e4ae139 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T21:40:35Z |
| publishDate | 2022-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-cbd4af3e9a7144f0b5e851369e4ae1392023-11-23T20:34:00ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-09-0123191148410.3390/ijms231911484cPlot: Contig-Plotting Visualization for the Analysis of Short-Read Nucleotide Sequence AlignmentsMingeun Ji0Yejin Kan1Dongyeon Kim2Jaehee Jung3Gangman Yi4Department of Multimedia Engineering, Dongguk University, Seoul 04620, KoreaDepartment of Multimedia Engineering, Dongguk University, Seoul 04620, KoreaDepartment of Multimedia Engineering, Dongguk University, Seoul 04620, KoreaDepartment of Information and Communication Engineering, Myongji University, Yongin-si 17058, KoreaDepartment of Multimedia Engineering, Dongguk University, Seoul 04620, KoreaAdvances in the next-generation sequencing technology have led to a dramatic decrease in read-generation cost and an increase in read output. Reconstruction of short DNA sequence reads generated by next-generation sequencing requires a read alignment method that reconstructs a reference genome. In addition, it is essential to analyze the results of read alignments for a biologically meaningful inference. However, read alignment from vast amounts of genomic data from various organisms is challenging in that it involves repeated automatic and manual analysis steps. We, here, devised cPlot software for read alignment of nucleotide sequences, with automated read alignment and position analysis, which allows visual assessment of the analysis results by the user. cPlot compares sequence similarity of reads by performing multiple read alignments, with FASTA format files as the input. This application provides a web-based interface for the user for facile implementation, without the need for a dedicated computing environment. cPlot identifies the location and order of the sequencing reads by comparing the sequence to a genetically close reference sequence in a way that is effective for visualizing the assembly of short reads generated by NGS and rapid gene map construction.https://www.mdpi.com/1422-0067/23/19/11484contig plottingread alignmentsequence alignment |
| spellingShingle | Mingeun Ji Yejin Kan Dongyeon Kim Jaehee Jung Gangman Yi cPlot: Contig-Plotting Visualization for the Analysis of Short-Read Nucleotide Sequence Alignments International Journal of Molecular Sciences contig plotting read alignment sequence alignment |
| title | cPlot: Contig-Plotting Visualization for the Analysis of Short-Read Nucleotide Sequence Alignments |
| title_full | cPlot: Contig-Plotting Visualization for the Analysis of Short-Read Nucleotide Sequence Alignments |
| title_fullStr | cPlot: Contig-Plotting Visualization for the Analysis of Short-Read Nucleotide Sequence Alignments |
| title_full_unstemmed | cPlot: Contig-Plotting Visualization for the Analysis of Short-Read Nucleotide Sequence Alignments |
| title_short | cPlot: Contig-Plotting Visualization for the Analysis of Short-Read Nucleotide Sequence Alignments |
| title_sort | cplot contig plotting visualization for the analysis of short read nucleotide sequence alignments |
| topic | contig plotting read alignment sequence alignment |
| url | https://www.mdpi.com/1422-0067/23/19/11484 |
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