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Big Data and Transcriptomics
Published in Shampa Sen, Leonid Datta, Sayak Mitra, Machine Learning and IoT, 2018
Sudharsana Sundarrajan, Sajitha Lulu, Mohanapriya Arumugam
RNA-Seq utilizes deep-sequencing technologies. The RNA of interest is isolated from the tissue of interest. The RNA is converted into a library of cDNA fragments, which are attached to the adaptors to one or both ends. Each molecule (with or without amplification) is sequenced to obtain short sequences from one end (single-end sequencing), or both ends (pair-end sequencing). Each read has a typical size between 30 and 400 bp, depending on the sequencing technology. The reads are aligned either to the reference transcripts or the reference genome, or assembled from a de novo genomic sequence (Figure 5.3). The results can be used to analyze both genomic and posttranslational mutations and mRNA expression levels of the genes. The sequencing platforms include Illumina IG, Applied Biosystems SOLiD, Roche 454 Life Science, or Helicos Biosciences tSMS. There are three main sequencing technologies including pyro-sequencing developed by 454 Life Sciences, reversible dye-terminator-based technology by Illumuna, and SOLiD technology by Applied Biosystems.17
Molecular Diagnostic Solutions in Algal Cultivation Systems
Published in Stephen P. Slocombe, John R. Benemann, Microalgal Production, 2017
Laura T. Carney, Robert C. McBride, Val H. Smith, Todd W. Lane
The handling of the raw sequence data from the sequencer is device dependent, and instruments generally come with data process and analysis software packages. Raw sequencing reads must pass through a series of quality control steps to remove low-quality and primer sequences and to mask low-complexity regions. Once this initial processing is complete, there are a number of software packages for micro-biome analysis including the QIIME (http://qiime.org/index.html) (Caporaso et al. 2010), mothur (Schloss et al. 2009), and RDP pyrosequencing pipeline designed for the analysis of 454 sequencing datasets.
Growth and genetic analysis of Pseudomonas BT1 in a high-thiourea environment reveals the mechanisms by which it restores the ability to remove ammonia nitrogen from wastewater
Published in Environmental Technology, 2022
Jingxuan Deng, Zhenxing Huang, Wenquan Ruan
Quality control was performed for raw sequencing data, and reads with a mean Q-score larger than seven and a length larger than 1000 bp were obtained for further analysis. Then, clean reads were assembled using Canu with the default parameters [20]. After error correction using Pilon [21], the draft assembly was checked for a circular structure and redundant parts were removed using Circlator with the ‘fixstart’ parameter to obtain the final genome assembly. The clean reads were mapped to the genome using Minimap2 [22] with the default parameters, and the sequencing depth of each site was determined using SAMtools. To confirm the plasmid, the genome sequences were aligned to the plasmid database using BLASTN with the parameters ‘-evalue 0.00001 -outfmt 6 -max_target_seqs 100000’. The reads were considered as a plasmid, with the length of alignment to the database accounting for more than 20% of the sequence length and the lengths of reads less than 1 MB.
A Chaotic Approach to Recognize the Characteristics of Genetic Codes of Covid Patients
Published in Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization, 2023
These are accessed in the FASTA (text-based format for identifying nucleotide sequences) file format. And these sequences are essentially obtained using Illumina sequencing technology, which is a molecular technique for evaluating the sequence of base pairs in DNA. It allows the comparison of DNA sequences to improve the understanding of normal and disease sequences and yields millions of quicker, cheaper and more accurate reads than other existing sequencing technologies.