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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.
HTML is the default output format for NCBI's web-page. Results for NCBI-BLAST are presented in graphical format with all the hits found, a table with sequence identifiers for the hits having scoring related data, along with the alignments for the sequence of interest and the hits received with analogous BLAST scores for these. [8]
Counter example generation GUI Graphical Specification Counter example visualization Software license Programming language used Platform, OS BLAST: Code analysis C: Monitor automata Yes No No No Free OCaml: Windows, Unix related CADP: Plain and probabilistic LOTOS, FC2, FSP, LNT AFMC, MCL, XTL SB, WB, BB, OE, STE, WTE, SE, tau*E Yes Yes No Yes
Output report types: plain text, HTML, XML. All report types support drill-down, to a user-controlled detail depth. The HTML report supports source code linking. Output reports can highlight items with coverage levels below user-provided thresholds. Coverage data obtained in different instrumentation or test runs can be merged.
JasperReports is an open source reporting library that can be embedded into any Java application. Features include: Scriptlets may accompany the report definition, [3] which the report definition can invoke at any point to perform additional processing. The scriptlet is built using Java, and has many hooks that can be invoked before or after ...
A BLAST variant called MegaBLAST indexes 4 databases to speed up alignments. [ 9 ] BLAT can extend on multiple perfect and near-perfect matches (default is 2 perfect matches of length 11 for nucleotide searches and 3 perfect matches of length 4 for protein searches), while BLAST extends only when one or two matches occur close together.
The guide tree in the initial versions of Clustal was constructed via a UPGMA cluster analysis of the pairwise alignments, hence the name CLUSTAL. [11] cf. [12] The first four versions of Clustal were numbered using Arabic numerals (1 to 4), whereas the fifth version uses the Roman numeral V. [11] cf. [13] [5] The next two versions proceed alphabetically using the Latin alphabet, with W ...