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Bioinformatics and Applications in Biotechnology
Published in Ram Chandra, R.C. Sobti, Microbes for Sustainable Development and Bioremediation, 2019
Once the genome has been sequenced and assembled properly, it needs annotation for identification of genes, mobile genetic elements, repeats, genome duplication, and diversity. Similarity search tools such as BLAST are used to identify obvious homologs, and more sophisticated tools such as GLIMMER (Gene Locator and Interpolated Markov ModelER), GENSCAN, and Artemis are some of the tools widely used for genome annotation. GLIMMER uses interpolated Markov models for microbial gene identification (Salzberg et al., 1998). The encyclopedia of DNA elements (ENCODE) project of National Human Genome Research Institute aims to identify all functional elements in human genome. Since only 1.5% of the genomic DNA is recognized as coding region, the role of the remaining component is not clear. The project aims to identify and fully characterize the regulome, which controls gene expression, and the findings will have major impact on understanding of the disease. Various bioinformatics tools are extensively used in the project to analyze and store the data so that it become useful during subsequent uses. A major outcome of the project is the FactorBook repository, which houses the database of more than 100 different transcription factors and their recognition sites in genomic DNA.
Isolation and genomic characterization of Klebsiella Lw3 with polychlorinated biphenyl degradability
Published in Environmental Technology, 2022
Di-Hua Zhu, Fang-Hong Nie, Qing-Lang Song, Wan Wei, Min Zhang, Yao Hu, Hong-Ying Lin, Dan-Ju Kang, Zhi-Bao Chen, Jin-Jun Chen
Complete genomic sequencing was performed by Shanghai Majorbio Bio-pharm Technology Company (PRC). HGAP 2.0 was used to filter and assemble the reads on the scaffold. Glimmer 3.02 was employed to predict the coding DNA sequences (CDSs) [18]. A BLAST search was then performed for CDSs across several commonly utilized databases including the NCBI NR database, Swiss-Prot, clusters of orthologous genes (COGs), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) [19–21]. CAZymes were identified, classified, and annotated using CAZyDB (http://www.cazy.org/).