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github.com - ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set.  Detail paper...

github.com - RestrictionDigest can simulate the reference genome digestion and generate comprehensive information of the simulation. It can simulate single-enzyme digestion, double-enzyme digestion and size selection process. It can also analyze multiple genomes...

www.softberry.com - FGENESH is the fastest (50-100 times faster than GenScan) and most accurate gene finder available - see the figure and the table below. In recent rice genome sequencing projects, it was cited "the most successful (gene finding) program (Yu et...

github.com - AccessSyRI: finding genomic rearrangements andlocal sequence differences from whole-genome assemblies SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for...

github.com - sourmash is a k-mer analysis multitool, and we aim to provide stable, robust programmatic and command-line APIs for a variety of sequence comparisons. Some of our special sauce includes: FracMinHash sketching, which enables accurate...

github.com - dna2bit is a software tool developed in C++11, leveraging the capabilities of OpenMP for parallel computing and the popcount technique for efficient bit manipulation. It has been thoroughly tested using the g++ and clang compilers on both Linux and...

Horizontal 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...

The research interest of this group include constraint programming, structure prediction in simplified protein models, investigation of protein energy landscapes, detection of RNA sequence/structure motifs, prediction and evaluation of alternative...

schizophreniaforum.org - For Alzheimer’s and other complex disorders, mining the genome for disease-associated variants is no longer the obstacle. The challenge nowadays is figuring out how the identified loci relate to disease. As reported last month in Nature and...

Pathway Analysis is usually performed with aim to enrich the genes with their functional information and reveal the underlying biological mechanisms pursue by genes. Pathway Analysis is not only limited to what biological pathways a particular set...