Abstract
rRNA-genes for phylogenetic classifications started to be used in 1980s first time by Carl Woese which made a ground breaking contribution to microbiome science. rRNA-genes are used to explore microbial diversity as well as a method for bacterial annotation. Many researchers followed rRNA-based analysis track as a central method in microbiology. Similarity based analyses use several new generations of Artificial Neural Networks to create classifiers against bacteria libraries to obtain high accuracies. By the time, the number of bacteria in these libraries increased enormously. In this article the accuracy of a classifier against Greenges library is tested. It has been shown by the author in previous articles that the Greengenes Classifier can be successfully used as a bioinformatics program that performs taxonomic classification of 16S rRNA gene sequences. In a previous article, the accuracy of the program is also tested when it is applied to common PCR products of the 16S rRNA variable regions, which are the only product of laboratories in microbiome projects. In this study, V1–V3 hyper variable regions from 16S rRNA genes of some known bacteria is taken from the work of A. Cosic. In this article we used Longest Common Subsequence similarity measure to classify bacterial 16S rRNA gene sequence short reads against the Greengenes library.
Highlights
Some bacteria, produce antibiotics; others live symbiotically in the guts of animals including humans, or elsewhere in their bodies, or on the roots of certain plants, bacteria are often found responsible from the human and animal diseases
In our study we have found that Greengenes is more consistent compared to the first two
Inner nodes are automatically assigned taxonomic ranks from NCBI supplemented with previous version of Greengenes taxonomy and CyanoDB (Komárek, et al, 2016)
Summary
Produce antibiotics; others live symbiotically in the guts of animals including humans, or elsewhere in their bodies, or on the roots of certain plants, bacteria are often found responsible from the human and animal diseases. Helping the breakdown of dead organic matter; they make up the base of the food chain in many environments Because of their extreme flexibility, capacity for rapid reproduction and growth, and contribution to the processes in the body of humans, and all living creatures, bacteria are of such immense importance in the life on the earth. Through their activities in the soil, bacteria contribute immensely to global energy conversion and the recycling of matter. Meta-genomic methods provided by nextgeneration sequencing technology such as Roche 454 (Cannone, et., al., 2002) and Illumina (Cole, et, al, 2007) have facilitated a remarkable expansion of our knowledge regarding uncultured bacteria (Yang et., a., 2016)
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
