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Genome Editing Tools
Published in Vineet Kumar, Vinod Kumar Garg, Sunil Kumar, Jayanta Kumar Biswas, Omics for Environmental Engineering and Microbiology Systems, 2023
Madhumita Barooah, Dibya Jyoti Hazarika
The accessibility to giant repositories associated with whole-genome sequencing as well as the understanding of previously decoded natural metabolic pathways allows redesigning of pathways through comparison with previously elucidated metabolic networks for remediation of toxic contaminants. Enzymes produced by different organisms are identified, and genes encoding those enzymes are assembled to construct novel metabolic pathways. Databases such as BRENDA (Placzek et al., 2017), KEGG (Kanehisa et al., 2017), MetaCyc (Caspi et al., 2016), and Rhea (Morgat et al., 2015) provide the information regarding the necessary enzymes for redesigning these pathways. Thus, already available pathways can be improved with additional enzymatic reactions for filling the gaps. These collective pathways are also called reference pathways and are very helpful for the comparison of various metabolic models of different organisms. BLAST (Altschul et al., 1990) – the sequence alignment program – enables the comparison of sequences by providing significant statistical similarities between the query sequences (nucleotide or protein) and the target database sequences. This approach identifies enzymes based on the fact that proteins with higher sequence homology are likely to perform similar functions.
Computation and Folding Predictions
Published in Peixuan Guo, Kirill A. Afonin, RNA Nanotechnology and Therapeutics, 2022
Basic Local Alignment Search Tool, as known as BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequence of proteins or the nucleotides of DNA and/or RNA sequences. A BLAST search enables a researcher to compare a subject protein or nucleotide sequence with a library or database of sequences and identify library sequences that resemble the query sequence above a certain threshold. It finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. BLAST can be used for several purposes, including identifying species, locating domains, establishing phylogeny, DNA mapping, and comparison.
Systems: packaging and applications
Published in Neil Collings, Fourier Optics in Image Processing, 2018
Sequence alignment is the correlation of a query sequence with a known database sequence. Query sequences were arranged as 2D images of varying sizes and correlated with 2D known database sequences in computer simulation of the VLC [58,63]. In the latter work, the bases were coded as grey levels, A as 65, C as 130, G as 195, and T as 255 (Figure 8.2a). The correlation result was compared with the state-of-the-art basic local alignment search tool (BLAST). BLAST achieves alignment by first locating the common sequences between the query and known database sequences. These are small, usually three base, sequences. Alignments based on these common locations are then scored and the high scoring alignments are then further searched with longer sequences. This local alignment technique has been preferred to previous global alignment approaches because the latter scale up as the square of the sequence length and also are sensitive to intrasequence rearrangements. The significant aspect of the correlation technique for aligning the sequences was that it was more robust to noise in the query sequence, which takes the form of individual changes in the bases at random locations, such as may be induced by genetic mutation. The robustness of the correlation approach can then be complemented with fast implementation in optical hardware in order to accommodate the increased computational complexity. Early start-up companies, such as Optalysis, are endeavouring to apply optical correlation techniques in this direction. Further work on the digital simulation of cross-correlation approaches includes the use of phase-only coding the four bases of both the query and the known sequence [217]. The bases were arranged evenly around the unit circle with the bp arranged in a complementary fashion (Figure 8.2b). The potential for infinities in the phase-only coding with sequences that repeat periodically was solved by zero padding the sequence to a prime number of bases [30]. Finally, an optical correlator based on a 1D acoustooptic scanner was used in a proof of concept system [32].
Detection of pathogenic bioaerosols and occupational risk in a Philippine landfill site
Published in Archives of Environmental & Occupational Health, 2018
Hera Angela M. Pagalilauan, Cielo Emar M. Paraoan, Pierangeli G. Vital
It was also established in this study that molecular methods using PCR and gene sequencing aid in better detection and understanding of the bioaerosols present in the site. Those that were tagged as unknown through culture methods were identified by molecular analysis. All of the BLAST results had an E value of zero, which defines the maximum significance of the match and least probability of chance match and false positives.15 The percent identity and percent cover of each sequence varied from 89% to 100% and 85% to 100%, respectively (Tables 2 and 3). Percent identity was said to be less sensitive in defining sequence similarity since it could define evolutionary distance only when homology has been established. Furthermore, no standard threshold is being followed globally.16 Despite these, the top match with the highest percent homology, percent cover, and total score as well as lowest E value was considered to be the identity of the isolate.
Kinetics of the biosorptive removal of chromium from water using mycelial biomass of Aspergillus oryzae
Published in Bioremediation Journal, 2022
Hamid Mukhtar, Iram Hina, Bushra Muneer, Umar Farooq Gohar, Muhammad Tayyab Akhtar
For taxonomical identification of fungal strain universal fungal primers ITS3 (5′ GCA TCG ATG AAG AAC GCA GC) and ITS4 (5′ TCC TCC GCT TAT TGA TAT GC) were used for amplification of 542 bp fragment of internal transcribed spacer 2 (ITS2) region of ribosomal DNA (White et al. 1990; Hinrikson et al. 2005). For sequence analysis sample was sent to School of Biological Sciences, University of the Punjab Lahore, Pakistan. The BLAST tools were used to find out the similarity of the sequenced gene.