Tags: Bioinformatics, Scalpel, Genetic, Variants, Discovery, Tool
3509 days ago
ChromHMM: Chromatin state discovery and characterization
ChromHMM is software for learning and characterizing chromatin states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover de novo the major re-occuring combinatorial and spatial patterns of marks. ChromHMM is based on a multivaria...Tags: Bioinformatics, ChromHMM, Chromatin, Discovery, Characterization, Chromosome
2536 days ago
CSBFinder: Discovery of colinear syntenic blocks across thousands of prokaryotic genomes
CSBFinder is a standalone Desktop java application with a graphical user interface, that can also be executed via command line. CSBFinder implements a novel methodology for the discovery, ranking, and taxonomic distribution analysis of colinear syntenic blocks (CSBs) - groups of genes that are c...Tags: CSBFinder, Discovery, colinear, syntenic, blocks, prokaryotic, genomes
1982 days ago
Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search
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 graphs assembly using colours can be unpractical fo...Tags: Π-cyc, Reference-free, SNP, Discovery, Application, Parallel, Graph, Search
1522 days ago
TARDIS: Toolkit for automated and rapid discovery of structural variants
tardis Toolkit for Automated and Rapid DIscovery of Structural variants Requirements zlib (http://www.zlib.net)mrfast (https://github.com/BilkentCompGen/mrfast)htslib (included as submodule; http://htslib.org/)Fetching tardis git clone https://github.com/BilkentCompGen/tardis.git --recursive ...Tags: TARDIS, Toolkit, automated, rapid, discovery, structural, variants
2485 days ago
Computational resources for TE discovery and TE detection
Transposable Elements (TEs) to genome structure and evolution as well as their impact on genome sequencing, assembly, annotation and alignment has generated increasing interest in developing new methods for their computational analysis. Following are the list of resource and location for TE dis...Tags: Computational, resources, TE, discovery, detection, Transposable, Elements (TEs)
2236 days ago
Tags: Breakpointer, local, mapping, artifacts, support, sequence, breakpoint, discovery, single-end, reads
2116 days ago
List of motif discovery tools !
In genetics, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance. For proteins, a sequence motif is distinguished from a structural motif, a motif formed by the three-dimensional arrangement of amino ac...Tags: motif, discovery, tools, protein, dna
1956 days ago
Tags: HGTector, automated, method, facilitating, genome-wide, discovery, putative, horizontal, gene, transfers
1894 days ago
RepeatModeler2: automated genomic discovery of transposable element families
RepeatModeler2 represents a valuable addition to the genome annotation toolkit that will enhance the identification and study of TEs in eukaryotic genome sequences. RepeatModeler2 is available as source code or a containerized package under an open license (https://github.com/Dfam-consortium/Repe...Tags: RepeatModeler2, automated, genomic, discovery, transposable, element, families
1579 days ago