Tools to detect synteny blocks regions among multiple genomes
...er can be used for finding regions syntenic across multiple genomes and measuring the extent of genome rearrangement using reversal distance as a measure. OrthoCluster (http://krono....2619 days ago
List of motif discovery tools !
...Tp -- computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues Identify and measure surface accessible pockets as...2002 days ago
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Awesome perl frameworks, libraries and software - PART 3
...l - RPerl Compiler petdance/bobby-tables - bobby-tables.com, the site for preventing SQL injections pshved/timeout - A script to measure and limit CPU time and memory...2503 days ago
List of In-silico Binding Site Prediction Tools
...voids buried in the interior of proteins. The measurement includes the area and vol...unbound split characteristic through the RMSD measurement. Furthermore, we conduct....bii.a-star.edu.sg/tankp/run_depth.html Depth measures the closest distance of a re...3753 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
...does not use population labels or genome-wide measures; designed to represent varia...carrying variant based on family’s raw measurements; accommodates de novo mu...ter SNP ID (rsID), choose population, region, measure for LD, threshold plot format...2918 days ago
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Tadpole is 250x faster than SPADes assembler !
...optionally perform error correction. correct: Error correct only. insert: Measure insert sizes....985 days ago
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GMASS: a novel measure for genomeassembly structural similarity
The GMASS score is a novel measure for representing structural similarity between two assemblies. It will contribute to the understanding of assembly output and developing de novo assemblers. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2710-zTags: GMASS, novel, measure, genome, assembly, structural, similarity
1857 days ago
auN: a new metric to measure assembly contiguity
Given a de novo assembly, we often measure the “average” contig length by N50. N50 is neither the real average nor median. It is the length of the contig such that this and longer contigs cover at least 50% of the assembly. A longer N50 indicates better contiguity. We can si...Tags: auN, new, metric, measure, assembly, contiguity
651 days ago
Comment on "Benchmarking Perl Module !"
...Perl Benchmark module, which provides a simple and standardized way to measure and compare the performance o...module. The Benchmark module provides a simple and standardized way to measure and compare the performance o...424 days ago
Comment on "Genome in a Bottle (GIAB) Consortium"
Benchmark (or "High-confidence") variant calls and regions:We developed an integration pipeline to utilize sequencing data generated by multiple technologies to generat...1569 days ago