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Bioinformatics tools to detect horizontal gene transfer (HGT) in genomes
Last updated 1053 days ago by AbhiHorizontal gene transfer (HGT), the “non-sexual movement of genetic material between two organisms” , is relatively common in prokaryotes and single-celled eukaryotes, but a number of factors combine to make it far rarer in...Ranbow: a haplotype assembler for polyploid genomes
By Jit 2368 days agowww.molgen.mpg.de - Ranbow is a haplotype assembler for polyploid genomes. It has been developed for the haplotype assembly of the hexaploid sweet potato genome, which is highly heterozygous. Ranbow can also be applied to other polyploid genomes. After a first phasing,...ALLHiC: Phasing and scaffolding polyploid genomes based on Hi-C data
By BioStar 2166 days agogithub.com - The major problem of scaffolding polyploid genome is that Hi-C signals are frequently detected between allelic haplotypes and any existing stat of art Hi-C scaffolding program links the allelic haplotypes together. To solve the problem, we developed...HaploTypo: a variant-calling pipeline for phased genomes
By Jit 1802 days agogithub.com - An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, most genetic variant calling tools do not explicitly account for haplotype structure. Here, we present HaploTypo, a pipeline tailored to resolve...CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
By Jit 1651 days agogithub.com - Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by...Published a dataset of 363 genomes from approximately 92 percent of bird families
By Jit 1466 days agoA research team published a dataset of 363 genomes from approximately 92 percent of bird families and showed the significance of sampling dense organisms for biodiversity research.OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes
By Abhi 573 days agoorthovenn3.bioinfotoolkits.net - OrthoVenn3 is a powerful tool for comparative genomics analysis, used as a web server for full genome comparisons, annotation, and evolutionary analysis of orthologous clusters across multiple species. It has already been used by thousands of users...PANNZER: a fully automated service for functional annotation of prokaryotic and eukaryotic proteins...
By BioStar 1564 days agoekhidna2.biocenter.helsinki.fi - PANNZER (Protein ANNotation with Z-scoRE) is a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function. PANNZER (Protein ANNotation with Z-scoRE) is a fully automated service for...Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search
By Jit 1763 days agogithub.com - Reference free SNP search for comparative population genomics: multiple samples run simultanously. **experimental phase, compiles and runs with OpenMPI-1.8.8 with Intel Compiler only Cycles enumeration (aka Bubbles) as part of de novo de bruijn...List of motif discovery tools !
By Neel 2197 days ago Comments (2)A DNA sequence motif represented as a sequence logo for the LexA-binding motif. I
