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C++ based molecule editor and visualizer for in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. Linux, macOS, Unix, Windows: 3-Clause BSD License: Open Chemistry Project: BEDtools "Genome arithmetic"—manipulation of coordinate sets and the extraction of sequences from a BED file. Linux: MIT
Whole genome assembly, restriction analysis, cloning, primer design, dotplot, much more >40 file formats imported and exported Proprietary, commercial; personal, floating ? Cross-platform - Mac, Windows, Linux Official website: Integrated Genome Browser (IGB) No No No Sequences and features from files, URLs, and arbitrary DAS and QuickLoad servers
Indexes the genome with a k-mer lookup table with full sensitivity up to an adjustable number of mismatches. It is best for mapping 15-60 bp sequences to a genome. No No Yes No, multiple processes per search 2003 QPalma Can use quality scores, intron lengths, and computation splice site predictions to perform and performs an unbiased alignment.
RGB value in the form R, G, B (e.g. 255,0,0) determining the display color of the annotation contained in the BED file No 10: blockCount: Number of blocks (e.g. exons) on the line of the BED file No 11: blockSizes: List of values separated by commas corresponding to the size of the blocks (the number of values must correspond to that of the ...
[9] [10] By the 2010s, the genome sequences of more than a thousand-human individuals (through the 1000 Genomes Project) and several model organisms became available. As such, genome annotation remains a major challenge for scientists investigating the human and other genomes. [21] [22]
Bowtie is a software package commonly used for sequence alignment and sequence analysis in bioinformatics. [3] The source code for the package is distributed freely and compiled binaries are available for Linux, macOS and Windows platforms.
The Human Pangenome Reference is a collection of genomes from a diverse cohort of individuals compiled by the Human Pangenome Reference Consortium (HPRC). This first draft pangenome comprises 47 phased, diploid assemblies from a diverse cohort of individuals and was intended to capture the genetic diversity of the human population. The ...
The HUGO Gene Nomenclature Committee (HGNC) is a committee of the Human Genome Organisation (HUGO) that sets the standards for human gene nomenclature. The HGNC approves a unique and meaningful name for every known human gene, [4] [5] based on a query of experts. In addition to the name, which is usually 1 to 10 words long, the HGNC also ...