Biology subjects

Panthee, D.

Publications and source records attributed to Panthee, D..

3 recordsLinked to original sources

bioRxiv2023

Improvements in the detection power of algorithms for analyzing next-generation sequencing based bulked segregant analysis data via estimating thresholds at the genomic region level

Next-generation sequencing based bulked segregant analysis (BSA-Seq) has been widely used in identifying genomic regions associated with a trait of interest. However, the most popular algorithms for BSA-Seq data analysis have relatively low detection power, and high sequencing depths are required for the detection of genomic regions linked to the trait. Here we estimated the confidence intervals/thresholds of the popular algorithms at the genomic region level and increased the detection power of these algorithms by at least 5 folds, which should drastically reduce the sequencing cost of BSA-Seq studies.

bioinformatics↗

bioRxiv2019

PyBSASeq: a novel, simple, and effective algorithm for BSA-Seq data analysis

Bulked segregant analysis (BSA), coupled with next generation sequencing (NGS), allows the rapid identification of both qualitative and quantitative trait loci (QTL), and this technique is referred to as BSA-Seq here. The current SNP index method and G-statistic method for BSA-Seq data analysis require relatively high sequencing coverage to detect major single nucleotide polymorphism (SNP)-trait associations, which leads to high sequencing cost. Here we developed a simple and effective algorithm for BSA-Seq data analysis and implemented it in Python, the program was named PyBSASeq. Using PyBSASeq, the likely trait-associated SNPs (ltaSNPs) were identified via Fishers exact test and then the ratio of the ltaSNPs to total SNPs in a chromosomal interval was used to identify the genomic regions that condition the trait of interest. The results obtained this way are similar to those generated by the current methods, but with more than five times higher sensitivity, which can reduce the sequencing cost by ~80% and makes BSA-Seq more applicable for the species with a large genome. Significance StatementBSA-Seq can be utilized to rapidly identify DNA polymorphismtrait associations, and PyBSASeq allows the detection of such associations at much lower sequencing coverage than the current methods, leading to lower sequencing cost and making BSA-Seq more accessible to the research community and more applicable to the species with a large genome.

bioinformatics↗

bioRxiv2018

Filter paper-based spin column for low throughput nucleic acid purification

We describe a method of recharging used spin column or assembling homemade spin column using filter paper as binding material for low throughput nucleic acid purification. We evaluated the efficiency of filter paper based spin columns in the purification of different type of nucleic acids. For instance, by following protocols of respective commercial kits, we found that filter paper to be a useful binding material for purification of many types of nucleic acids, including plant genomic DNA, plant total RNA, PCR product, and DNA from agarose gels. We also found that filter paper has a weak binding affinity to plasmid DNA in tested miniprep protocols. Also, we present the protocols of using filter paper recharged spin column or homemade spin column for low throughput purification of plant genomic DNA and plant total RNA with commercial kit buffer leftover and less expensive homemade buffer.

molecular biology↗