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By Poonam Mahapatra 3031 days agosourceforge.net - GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior...GeneOverlap: An R package to test and visualize gene overlaps
By Jit 2823 days agobioconductor.org - Overlapping gene lists can reveal biological meanings and may lead to novel hypotheses. For example, histone modification is an important cellular mechanism that can pack and re-pack chromatin. By making the chromatin structure more dense or loose,...ShadowCaster: a hybrid approach for the detection of horizontal gene transfer events in prokaryotes
By Jit 2258 days agogithub.com - ShadowCaster implements an evolutionary model to calculate Bayesian likelihoods for each ‘alien genes’ with an unusual sequence composition according to the host genome background to detect HGT events in...homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes
By Abhi 1204 days agogithub.com - This tutorial describes the usage of homologizer to phase gene copies into polyploid subgenomes. The tutorial is an abbreviated version of a soon-to-be published paper in Methods in Molecular Biology. Please see that paper for many more...Now time is come to revolutionize amino acid sequencing by Nanopore technology
By Rahul Agarwal 4548 days agowww.eurekalert.org - Amino acid sequencing by Nanopore recognition tunneling methodMaq: Mapping and Assembly with Quality
By Jit 3588 days agomaq.sourceforge.net - Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences. Maq is a project hosted by SourceForge.net. The project page is available athttp://sourceforge.net/projects/maq/....The "Ifs" and "Buts" of NGS Quality Control and Trimming
By BioStar 624 days agoNGS quality control and trimming are essential steps to ensure reliable and accurate data for analysis. While the "ifs" highlight the clear benefits of these steps, the "buts" remind us of the potential pitfalls. By adopting best practices and...Indexcov: fast coverage quality control for whole-genome sequencing
By Jit 2943 days ago Comments (1)github.com - indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large-scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a...Filtlong: quality filtering tool for long reads
By Radha Agarkar 2320 days agogithub.com - Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the...Mike Ritchie Lab
Mike Ritchie Lab primary research focus is the detection of susceptibility genes for common diseases such as cancer, diabetes, hypertension, and cardiovascular disease, among others. The approaches will involve the development and application of new...
