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Open Chemistry Project: BEDtools "Genome arithmetic"—manipulation of coordinate sets and the extraction of sequences from a BED file. Linux: MIT: QuinlanLab, University of Utah: Bioclipse: Visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP) Linux, macOS, Windows [1] Eclipse Public: The Bioclipse ...
Open-source, written in pure Java; supports all platforms with no recompilation and no other dependencies. ContextMap was developed to overcome some limitations of other mapping approaches, such as resolution of ambiguities. The central idea of this tool is to consider reads in gene expression context, improving this way alignment accuracy.
This server includes many bioinformatics tools that are widely useful in many areas of genomics research. Users can create logins, and save histories, workflows, and datasets on the server. These saved items can also be shared with others. As open-source software that can be downloaded, installed and customized to address specific needs. [20]
NGS platforms Platform Template preparation Chemistry Max read length (bases) Run times (days) Max Gb per Run Roche 454 Clonal-emPCR Pyrosequencing 400‡ 0.42 0.40-0.60 GS FLX Titanium Clonal-emPCR Pyrosequencing 400‡ 0.42 0.035 Illumina MiSeq Clonal Bridge Amplification Reversible Dye Terminator 2x300 0.17-2.7 15 Illumina HiSeq
Open source software provides a platform for computational biology where everyone can access and benefit from software developed in research. PLOS cites [citation needed] four main reasons for the use of open source software: Reproducibility: This allows for researchers to use the exact methods used to calculate the relations between biological ...
The source code for the package is distributed freely and compiled binaries are available for Linux, macOS and Windows platforms. As of 2017, the Genome Biology paper describing the original Bowtie method has been cited more than 11,000 times. [3] Bowtie is open-source software and is currently maintained by Johns Hopkins University.
GenMAPP was developed by biologists and is focused on pathway visualization for bench biologists. Unlike many other computational systems biology tools, GenMAPP is not designed for cell/systems modeling; it focuses on the immediate needs of bench biologists by enabling them to rapidly interpret genomic data with an intuitive, easy-to-use interface.
Uses adaptative seeds and copes more efficiently with repeat-rich sequences (e.g. genomes). For example: it can align reads to genomes without repeat-masking, without becoming overwhelmed by repetitive hits. Yes Yes Yes Yes Free, GPL [46] 2011 MAQ Ungapped alignment that takes into account quality scores for each base. Free, GPL: mrFAST, mrsFAST