Comparison of DNA Sequences with Protein Sequences

Pearson, William R.; Wood, Todd Charles; Zhang, Zheng; Miller, Webb

doi:10.1006/geno.1997.4995

Cited by 561 publications

(393 citation statements)

References 19 publications

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“…Upon receipt of the raw sequences, we used the FastX toolkit to visualize the data quality, specifically the quality scores, read length, per bp quality, and per read quality (Pearson, Wood, Zhang, & Miller, 1997). We merged the raw paired‐end reads with the software PEAR v 0.9.6 (Zhang, Kobert, Flouri, & Stamatakis, 2014) using a quality threshold (Phred score) of 10 for trimming the reads and detected sequence chimeras de novo using default parameters of the UCHIME algorithm (Edgar, Haas, Clemente, Quince, & Knight, 2011).…”

Section: Methodsmentioning

confidence: 99%

Gut microflora may facilitate adaptation to anthropic habitat: A comparative study in Rattus

Varudkar

Ramakrishnan

2018

Ecology and Evolution

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Anthropophilic species (“commensal” species) that are completely dependent upon anthropic habitats experience different selective pressures particularly in terms of food than their noncommensal counterparts. Using a next‐generation sequencing approach, we characterized and compared the gut microflora community of 53 commensal Rattus rattus and 59 noncommensal Rattus satarae captured in 10 locations in the Western Ghats, India. We observed that, while species identity was important in characterizing the microflora communities of the two Rattus hosts, environmental factors also had a significant effect. While there was significant geographic variation in the microflora of the noncommensal R. satarae, there was no effect of geographic distance on gut microflora of the commensal R. rattus. Interestingly, host genetic distance did not significantly influence the community in either Rattus hosts. Collectively, these results indicate that a shift in habitat is likely to result in a change in the gut microflora community and imply that the gut microflora is a complex trait, influenced by various parameters in different habitats.

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Section: Methodsmentioning

confidence: 99%

Gut microflora may facilitate adaptation to anthropic habitat: A comparative study in Rattus

Varudkar

Ramakrishnan

2018

Ecology and Evolution

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“…Primer design was checked in Oligo 4.0 for Macintosh. Sequence data were analysed using the Wisconsin GCG package Version 10, Laser Gene Package for the Macintosh version 1.58 (DNAStar),  (Pearson et al, 1997),  (Altshchul et al, 1990),   (Higgins et al, 1994) and PHDsec (Columbia University ; http :\\ www2.ebi.ac.uk). Hydrophobicity domains were determined using   (version 1.1).…”

Section: Methodsmentioning

confidence: 99%

The complete cps gene cluster from Streptococcus thermophilus NCFB 2393 involved in the biosynthesis of a new exopolysaccharide

et al. 2000

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The cpsFGHIJKL genes from the cps cluster of Streptococcus thermophilus NCFB 2393 involved in the biosynthesis of EPS were identified, cloned and nucleotide sequenced. The complete cps cluster is contained on an " 11 2 kb chromosomal region which contains 12 ORFs, including the previously cloned cpsABCDE genes. Functions were assigned to some of the predicted gene products on the basis of homology to known sequences as follows : cpsK encodes a protein thought to be involved in the polymerization and export of the polysaccharide ; cpsE, cpsF, cpsG, cpsH, cpsI and cpsJ encode putative sugar transferases. Two insertion sequences, IS1193 and ISS1, were identified within and flanking the 3' end of the cps cluster respectively. Analysis of the expression of the cpsE gene in Escherichia coli demonstrated that it encodes a glucose-1-phosphate transferase ; the enzyme which catalyses the first step in EPS biosynthesis in S. thermophilus NCFB 2393.

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“…For libraries that generated from small RNA (PAR-CLIP and ribosome profiling), the adapters were trimmed by using FASTX-Toolkit [43]. The deep sequencing data were mapped to Human genome version hg38 by Tophat version 2.0 [44] without any gaps and allowed for at most two mismatches.…”

Section: Sequencing Data Analysismentioning

confidence: 99%