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BioSmalltalk
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BioSmalltalk is a pure object environment for developing bioinformatics scripts and applications in Smalltalk. It's open source and based in the Pharo Smalltalk environment. Features * IUPAC alphabets API. * Basic biological objects: BioSequence, BioSeqRecord, BioAlignment, BioFastaRecord, BioCodonTable, etc. * BLAST objects for querying and filtering results from NCBI or locally. Tests and examples are included. * Entrez system API with tests and examples * Writers for formatted files: CSV, FASTA, Haploview, Fluxus Network, etc. * Parsers for reading formatted files: XML, FASTA, NCBI identifiers or DNA sequences with degenerate bases as sent from Illumina reports, i.e. of the form : 'ACTG' or 'ATTA'. * Tools for creating custom views of objects using inspectors, explorers or browsers. |
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