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genome--bacterial
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The performances of the chi-square test and complexity measures for signal recognition in biological sequences
, Article Journal of Theoretical Biology ; Volume 251, Issue 2 , 2008 , Pages 380-387 ; 00225193 (ISSN) ; Kargar, M ; Sheari, A ; Poormohammadi, H ; Sadeghi, M ; Pezeshk, H ; Eslahchi, C ; Sharif University of Technology
2008
Abstract
With large amounts of experimental data, modern molecular biology needs appropriate methods to deal with biological sequences. In this work, we apply a statistical method (Pearson's chi-square test) to recognize the signals appear in the whole genome of the Escherichia coli. To show the effectiveness of the method, we compare the Pearson's chi-square test with linguistic complexity on the complete genome of E. coli. The results suggest that Pearson's chi-square test is an efficient method for distinguishing genes (coding regions) form pseudogenes (noncoding regions). On the other hand, the performance of the linguistic complexity is much lower than the chi-square test method. We also use the...
Genome annotation and comparative genomic analysis of Bacillus subtilis MJ01, a new bio-degradation strain isolated from oil-contaminated soil
, Article Functional and Integrative Genomics ; Volume 18, Issue 5 , 2018 , Pages 533-543 ; 1438793X (ISSN) ; Niazi, A ; Deihimi, T ; Taghavi, S. M ; Ayatollahi, S ; Ebrahimie, E ; Sharif University of Technology
Springer Verlag
2018
Abstract
One of the main challenges in elimination of oil contamination from polluted environments is improvement of biodegradation by highly efficient microorganisms. Bacillus subtilis MJ01 has been evaluated as a new resource for producing biosurfactant compounds. This bacterium, which produces surfactin, is able to enhance bio-accessibility to oil hydrocarbons in contaminated soils. The genome of B. subtilis MJ01 was sequenced and assembled by PacBio RS sequencing technology. One big contig with a length of 4,108,293 bp without any gap was assembled. Genome annotation and prediction of gene showed that MJ01 genome is very similar to B. subtilis spizizenii TU-B-10 (95% similarity). The comparison...