<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/40099?offset=290 https://bioinformaticsonline.com/bookmarks/view/28891/lumpy Thu, 25 Aug 2016 08:05:02 -0500 https://bioinformaticsonline.com/bookmarks/view/28891/lumpy <![CDATA[LUMPY]]> A probabilistic framework for structural variant discovery.

Ryan M Layer, Colby Chiang, Aaron R Quinlan, and Ira M Hall. 2014. "LUMPY: a Probabilistic Framework for Structural Variant Discovery." Genome Biology 15 (6): R84. doi:10.1186/gb-2014-15-6-r84.

More at https://github.com/arq5x/lumpy-sv

Address of the bookmark: https://github.com/arq5x/lumpy-sv

]]> Shruti Paniwala https://bioinformaticsonline.com/bookmarks/view/34940/jpred4-a-protein-secondary-structure-prediction-server Fri, 29 Dec 2017 16:14:28 -0600 https://bioinformaticsonline.com/bookmarks/view/34940/jpred4-a-protein-secondary-structure-prediction-server <![CDATA[JPred4: A Protein Secondary Structure Prediction Server]]> JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction.

Address of the bookmark: http://www.compbio.dundee.ac.uk/jpred4/

]]> Poonam Mahapatra https://bioinformaticsonline.com/bookmarks/view/36849/glean-an-unsupervised-learning-system-to-integrate-disparate-sources-of-gene-structure-evidence Sat, 02 Jun 2018 07:38:33 -0500 https://bioinformaticsonline.com/bookmarks/view/36849/glean-an-unsupervised-learning-system-to-integrate-disparate-sources-of-gene-structure-evidence <![CDATA[GLEAN: an unsupervised learning system to integrate disparate sources of gene structure evidence]]> 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 training.

Address of the bookmark: https://sourceforge.net/projects/glean-gene/

]]> Poonam Mahapatra https://bioinformaticsonline.com/bookmarks/view/43801/smudgeplot-inference-of-ploidy-and-heterozygosity-structure-using-whole-genome-sequencing-data Fri, 25 Feb 2022 04:42:09 -0600 https://bioinformaticsonline.com/bookmarks/view/43801/smudgeplot-inference-of-ploidy-and-heterozygosity-structure-using-whole-genome-sequencing-data <![CDATA[Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data]]> This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc.

Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example:

smudgeexample

Address of the bookmark: https://github.com/KamilSJaron/smudgeplot

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