Sayak Banerjee, Amity University Kolkata
In the year 1977, the Archaebacteria or Archaea, the third domain of life separate from Bacteria and Eukaryota, was proposed by Carl Woese and George Fox. They had analyzed small subunit ribosomal RNA ( SSU rRNA) oligonucleotide fragments from 13 microbes before establishing this proposal. In the late 1980s, the use of SSU rRNA to describe phylogenetic relationships continued and had significantly expanded.
Many environmental studies target SSU rRNA as a phylogenetic marker gene. They are aimed to determine the diversity of life in a given environment. These studies are common and as a result, there are millions of prokaryotic SSU rRNA sequences in a public database. When rRNA sequences are submitted to public databases like GenBank, quality control is essential to prevent subsequent errors in sequencing and sequence annotation. Hence, researchers from NCBI have reported their description of Ribovore, a software package for the curation and validation of rRNA sequence collection and submission respectively in the journal of BMC Bioinformatics.
Development of Ribovore:
BLASTN similarity searches have been in use for contrasting the submitted rRNA sequences against databases of credible rRNA sequences. After the curation with Ribovore began, the databases were more comprehensive. Before the Ribovore project was developed, checking for eukaryotic SSU rRNA or large subunit (LSU) rRNA sequences was not easy and time-consuming. There was no appropriate BLASTN database for validating the submission of those genes.
The development of Ribovore as an alternative sequence validation system for rRNA included four objectives for the potential advancement over the existing one. First, the system should be as accurate as possible in determining whether sequences are passing (accepted) or failing (not accepted). Second, the system should be available as a separate tool for the submitters to run their sequences before submission, thus saving time. Third, it should be a general system that would assist additional taxonomic groups and rRNA genes. Fourth, the system should have the potential to generate high-quality non-redundant sequences by adding tests and increasing its difficulty.
Salient features of Ribovore:
Ribovore includes many programs intended for different tasks, all of which are related. Each of the programs has deterministic criteria based on which a sequence passes or fails. rRNA_SENSOR is a simplified version of the prior BLASTN-based system that is faster and more easily portable for archaeal and bacterial SSU rRNA. RIBOTYPER compares each input sequence against a library of profile hidden Markov models (profile HMMs) or covariance models (CMs). This makes it a more powerful technique than a single-sequence-based BLASTN algorithm.
RIBOALIGNER was implemented to selectively determine full-length RNA sequences that extend up to the gene boundaries. Following that, multiple alignments are created and only those sequences are chosen that are passed based on those alignments. Finally, RIBODBMAKER was developed to choose a non-redundant set of high-quality, full-length sequences based on a series of tests.
Success of Ribovore:
The scientists said that at NCBI since 2018, Ribovore has been employed for checking the quality of incoming submissions to be used as BLASTN databases. The software package has been manually utilized by GenBank indexers whenever uncertain results were obtained for the BLASTN analysis of other rRNAs. A subset of the BLASTN databases, created by Ribovore, is used in more than 2000 web blastn runs per day. It has been used to check millions of 16S archaeal and bacterial SSU rRNA sequences through the year 2020. They mentioned that their report regarding the development and implementation of Ribovore will achieve a novel understanding of how rRNA sequences are curated in GenBank, RefSeq, and associated resources.
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Reference:
- Schäffer, A. A., McVeigh, R., Robbertse, B., Schoch, C. L., Johnston, A., Underwood, B. A., Karsch-Mizrachi, I., & Nawrocki, E. P. (2021). Ribovore: Ribosomal RNA sequence analysis for GenBank submissions and database curation. BMC Bioinformatics, 22(1), 400. https://doi.org/10.1186/s12859-021-04316-z
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Author info:
Sayak Banerjee is a 3rd-year Biotechnology Engineering Student with a great interest in Immunology and Molecular genetics. He is a creative scientific writer in Bioxone with an inclination towards gaining knowledge regarding vast sections of Biotechnology and emphasizing himself in various wet lab skills.
Publications:
- https://bioxone.in/news/worldnews/car-t-cells-scientists-discover-on-off-switches-for-cell-immunotherapy/
- https://bioxone.in/news/worldnews/neutrophil-derived-nanovesicles-a-novel-drug-delivery-system/
- https://bioxone.in/news/worldnews/pig-to-human-heart-transplantation-a-solution-to-the-rarity-of-donor-organs/
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