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BioJava is an open-source software project dedicated to provide Java tools to process biological data. [1] [2] [3] BioJava is a set of library functions written in the programming language Java for manipulating sequences, protein structures, file parsers, Common Object Request Broker Architecture (CORBA) interoperability, Distributed Annotation System (DAS), access to AceDB, dynamic ...
BLAST output parsers: MuSeqBox, Zerg, BioParser, BLAST-Explorer, SequenceServer; specialized BLAST-related tools: MEGAN, BLAST2GENE, BOV, Circoletto; Example visualizations of BLAST results are shown in Figure 4 and 5. Fig. 4 Circos-style visualization of BLAST results generated using SequenceServer software.
Collaborative project GenGIS: Application that allows combining digital map data with information about biological sequences collected from the environment Windows, macOS: GPL: Collaborative project Genomespace: Centralized web application that provides data format transformations and facilitates connections with other bioinformatics tools Web ...
The source database may be in either FASTA or ASN.1 format. Although the FASTA format is most often used as input to formatdb, the use of ASN.1 is advantageous for those who are using ASN.1 as the common source for other formats such as the GenBank report. The opposite of operation of formatdb, extracting sequences from a blast formatted ...
The fourth is a great example of how interactive graphical tools enable a worker involved in sequence analysis to conveniently execute a variety if different computational tools to explore an alignment's phylogenetic implications; or, to predict the structure and functional properties of a specific sequence, e.g., comparative modelling.
The FAST4 format was invented as a derivative of the FASTQ format where each of the 4 bases (A,C,G,T) had separate probabilities stored. It was part of the Swift basecaller, an open source package for primary data analysis on next-gen sequence data "from images to basecalls". The FAST5 format was invented as an extension of the FAST4 format.
No. 5 Indiana takes its unbeaten record to Ohio Stadium to take on No. 2 Ohio State. Here is how to watch Saturday's game.
Multiplatform open source application for the solution of physical problems based on the Hermes library: University of West Bohemia: 3.2: 2014-03-03: GNU GPL: Free: Linux, Windows: CalculiX: It is an Open Source FEA project. The solver uses a partially compatible ABAQUS file format. The pre/post-processor generates input data for many FEA and ...