i-rDNA: alignment-free algorithm for rapid <it>in silico</it> detection of ribosomal gene fragments from metagenomic sequence data sets
<p>Abstract</p> <p>Background</p> <p>Obtaining accurate estimates of microbial diversity using rDNA profiling is the first step in most metagenomics projects. Consequently, most metagenomic projects spend considerable amounts of time, money and manpower for experimental...
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| Format: | Article |
| Language: | English |
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BMC
2011-11-01
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| Series: | BMC Genomics |
| _version_ | 1819122525233217536 |
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| author | Mohammed Monzoorul Ghosh Tarini Chadaram Sudha Mande Sharmila S |
| author_facet | Mohammed Monzoorul Ghosh Tarini Chadaram Sudha Mande Sharmila S |
| author_sort | Mohammed Monzoorul |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Obtaining accurate estimates of microbial diversity using rDNA profiling is the first step in most metagenomics projects. Consequently, most metagenomic projects spend considerable amounts of time, money and manpower for experimentally cloning, amplifying and sequencing the rDNA content in a metagenomic sample. In the second step, the entire genomic content of the metagenome is extracted, sequenced and analyzed. Since DNA sequences obtained in this second step also contain rDNA fragments, rapid <it>in silico</it> identification of these rDNA fragments would drastically reduce the cost, time and effort of current metagenomic projects by entirely bypassing the experimental steps of primer based rDNA amplification, cloning and sequencing. In this study, we present an algorithm called i-rDNA that can facilitate the rapid detection of 16S rDNA fragments from amongst millions of sequences in metagenomic data sets with high detection sensitivity.</p> <p>Results</p> <p>Performance evaluation with data sets/database variants simulating typical metagenomic scenarios indicates the significantly high detection sensitivity of i-rDNA. Moreover, i-rDNA can process a million sequences in less than an hour on a simple desktop with modest hardware specifications.</p> <p>Conclusions</p> <p>In addition to the speed of execution, high sensitivity and low false positive rate, the utility of the algorithmic approach discussed in this paper is immense given that it would help in bypassing the entire experimental step of primer-based rDNA amplification, cloning and sequencing. Application of this algorithmic approach would thus drastically reduce the cost, time and human efforts invested in all metagenomic projects.</p> <p>Availability</p> <p>A web-server for the i-rDNA algorithm is available at <url>http://metagenomics.atc.tcs.com/i-rDNA/</url></p> |
| first_indexed | 2024-12-22T06:53:50Z |
| format | Article |
| id | doaj.art-cc9a6e66220e464783511933e4908b9f |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-22T06:53:50Z |
| publishDate | 2011-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-cc9a6e66220e464783511933e4908b9f2022-12-21T18:35:02ZengBMCBMC Genomics1471-21642011-11-0112Suppl 3S1210.1186/1471-2164-12-S3-S12i-rDNA: alignment-free algorithm for rapid <it>in silico</it> detection of ribosomal gene fragments from metagenomic sequence data setsMohammed MonzoorulGhosh TariniChadaram SudhaMande Sharmila S<p>Abstract</p> <p>Background</p> <p>Obtaining accurate estimates of microbial diversity using rDNA profiling is the first step in most metagenomics projects. Consequently, most metagenomic projects spend considerable amounts of time, money and manpower for experimentally cloning, amplifying and sequencing the rDNA content in a metagenomic sample. In the second step, the entire genomic content of the metagenome is extracted, sequenced and analyzed. Since DNA sequences obtained in this second step also contain rDNA fragments, rapid <it>in silico</it> identification of these rDNA fragments would drastically reduce the cost, time and effort of current metagenomic projects by entirely bypassing the experimental steps of primer based rDNA amplification, cloning and sequencing. In this study, we present an algorithm called i-rDNA that can facilitate the rapid detection of 16S rDNA fragments from amongst millions of sequences in metagenomic data sets with high detection sensitivity.</p> <p>Results</p> <p>Performance evaluation with data sets/database variants simulating typical metagenomic scenarios indicates the significantly high detection sensitivity of i-rDNA. Moreover, i-rDNA can process a million sequences in less than an hour on a simple desktop with modest hardware specifications.</p> <p>Conclusions</p> <p>In addition to the speed of execution, high sensitivity and low false positive rate, the utility of the algorithmic approach discussed in this paper is immense given that it would help in bypassing the entire experimental step of primer-based rDNA amplification, cloning and sequencing. Application of this algorithmic approach would thus drastically reduce the cost, time and human efforts invested in all metagenomic projects.</p> <p>Availability</p> <p>A web-server for the i-rDNA algorithm is available at <url>http://metagenomics.atc.tcs.com/i-rDNA/</url></p> |
| spellingShingle | Mohammed Monzoorul Ghosh Tarini Chadaram Sudha Mande Sharmila S i-rDNA: alignment-free algorithm for rapid <it>in silico</it> detection of ribosomal gene fragments from metagenomic sequence data sets BMC Genomics |
| title | i-rDNA: alignment-free algorithm for rapid <it>in silico</it> detection of ribosomal gene fragments from metagenomic sequence data sets |
| title_full | i-rDNA: alignment-free algorithm for rapid <it>in silico</it> detection of ribosomal gene fragments from metagenomic sequence data sets |
| title_fullStr | i-rDNA: alignment-free algorithm for rapid <it>in silico</it> detection of ribosomal gene fragments from metagenomic sequence data sets |
| title_full_unstemmed | i-rDNA: alignment-free algorithm for rapid <it>in silico</it> detection of ribosomal gene fragments from metagenomic sequence data sets |
| title_short | i-rDNA: alignment-free algorithm for rapid <it>in silico</it> detection of ribosomal gene fragments from metagenomic sequence data sets |
| title_sort | i rdna alignment free algorithm for rapid it in silico it detection of ribosomal gene fragments from metagenomic sequence data sets |
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