Clustering 16S rRNA for OTU prediction: A similarity based method
To study the phylogeny and taxonomy of samples from complex environments Next-generation sequencing (NGS)-based 16S rRNA sequencing , which has been successfully used jointly with the PCR amplification and NGS technology. First step for many downstream analyses is clustering 16S rRNA sequences into...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
Research and Development Academy
2019-12-01
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| Series: | Heritage and Sustainable Development |
| Online Access: | https://hsd.ardascience.com/index.php/journal/article/view/4 |
| _version_ | 1831586974796873728 |
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| author | Mehmet Can Osman Gürsoy |
| author_facet | Mehmet Can Osman Gürsoy |
| author_sort | Mehmet Can |
| collection | DOAJ |
| description | To study the phylogeny and taxonomy of samples from complex environments Next-generation sequencing (NGS)-based 16S rRNA sequencing , which has been successfully used jointly with the PCR amplification and NGS technology. First step for many downstream analyses is clustering 16S rRNA sequences into operational taxonomic units (OTUs). Heuristic clustering is one of the most widely employed approaches for generating OTUs in which one or more seed sequences to represent each cluster are selected. In this work we chose five random seeds for each cluster from a genes library, and we present a novel distance measure to cluster bacteria in the sample. Artificially created sets of 16S rRNA genes selected from databases are successfully clustered with more than %98 accuracy, sensitivity, and specificity. |
| first_indexed | 2024-12-17T21:46:27Z |
| format | Article |
| id | doaj.art-193a4a40b19c479aa01413eeffe69fb3 |
| institution | Directory Open Access Journal |
| issn | 2712-0554 |
| language | English |
| last_indexed | 2024-12-17T21:46:27Z |
| publishDate | 2019-12-01 |
| publisher | Research and Development Academy |
| record_format | Article |
| series | Heritage and Sustainable Development |
| spelling | doaj.art-193a4a40b19c479aa01413eeffe69fb32022-12-21T21:31:26ZengResearch and Development AcademyHeritage and Sustainable Development2712-05542019-12-0112788310.37868/hsd.v1i2.44Clustering 16S rRNA for OTU prediction: A similarity based methodMehmet CanOsman GürsoyTo study the phylogeny and taxonomy of samples from complex environments Next-generation sequencing (NGS)-based 16S rRNA sequencing , which has been successfully used jointly with the PCR amplification and NGS technology. First step for many downstream analyses is clustering 16S rRNA sequences into operational taxonomic units (OTUs). Heuristic clustering is one of the most widely employed approaches for generating OTUs in which one or more seed sequences to represent each cluster are selected. In this work we chose five random seeds for each cluster from a genes library, and we present a novel distance measure to cluster bacteria in the sample. Artificially created sets of 16S rRNA genes selected from databases are successfully clustered with more than %98 accuracy, sensitivity, and specificity.https://hsd.ardascience.com/index.php/journal/article/view/4 |
| spellingShingle | Mehmet Can Osman Gürsoy Clustering 16S rRNA for OTU prediction: A similarity based method Heritage and Sustainable Development |
| title | Clustering 16S rRNA for OTU prediction: A similarity based method |
| title_full | Clustering 16S rRNA for OTU prediction: A similarity based method |
| title_fullStr | Clustering 16S rRNA for OTU prediction: A similarity based method |
| title_full_unstemmed | Clustering 16S rRNA for OTU prediction: A similarity based method |
| title_short | Clustering 16S rRNA for OTU prediction: A similarity based method |
| title_sort | clustering 16s rrna for otu prediction a similarity based method |
| url | https://hsd.ardascience.com/index.php/journal/article/view/4 |
| work_keys_str_mv | AT mehmetcan clustering16srrnaforotupredictionasimilaritybasedmethod AT osmangursoy clustering16srrnaforotupredictionasimilaritybasedmethod |