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Biopython can read and write to a number of common sequence formats, including FASTA, FASTQ, GenBank, Clustal, PHYLIP and NEXUS. When reading files, descriptive information in the file is used to populate the members of Biopython classes, such as SeqRecord. This allows records of one file format to be converted into others.
Biopython: Python language toolkit Cross-platform: Biopython [1] Open Bioinformatics Foundation: BioRuby: Ruby language toolkit ? GPL v2 or Ruby: Open Bioinformatics Foundation: BLAST: Algorithm and program for comparing primary biological sequence information, including DNA and protein sequences. Cross-platform: Public domain
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 ...
GenBank (National Center for Biotechnology Information) DDBJ (Japan), GenBank (USA) and European Nucleotide Archive (Europe) are repositories for nucleotide sequence data from all organisms . All three accept nucleotide sequence submissions, and then exchange new and updated data on a daily basis to achieve optimal synchronisation between them.
The DDBJ/EMBL-EBI/GenBank synchronization is maintained according to a number of guidelines which are produced and published by an International Advisory Board. [3] The guidelines consist of a common definition of the feature tables [ 4 ] for the databases, which regulate the content and syntax of the database entries, [ 5 ] in the form of a ...
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A DNA dot plot of a human zinc finger transcription factor (GenBank ID NM_002383), showing regional self-similarity. The main diagonal represents the sequence's alignment with itself; lines off the main diagonal represent similar or repetitive patterns within the sequence. This is a typical example of a recurrence plot.
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