Ann: CoreBio 0.4

GavinCrooks at GavinCrooks at
Mon Sep 11 09:59:30 CEST 2006

Announcing CoreBio 0.4
CoreBio home page:


CoreBio is an open source python library for bioinformatics and
computational biology, designed to be fast, compact, reliable and easy
to use. Currently, CoreBio includes code to store and manipulate
protein and DNA sequences, read and write many common biological
sequence formats, read blast reports and access other computational and
database resources.

The CoreBio project welcomes additional suggestions, code and

This release includes the following modules:

    - data: Standard information used in computational biology.
    - matrix: Arrays indexed by alphabetic strings.
    - moremath: Various bits of useful math not in the standard

                python library.
    - resource: Access to programs, complex file formats and
        - astral: ASTRAL dataset IO.
        - scop: SCOP: Structural Classification of Proteins IO.
        - stride: STRIDE: Protein secondary structure assignment

                from atomic coordinates.
    - seq: Alphabetic sequences and associated tools and data.
    - seq_io: Sequence file reading and writing.
        - array_io: Read and write arrays of sequence data.
        - clustal_io: Read the CLUSTAL sequence file format.
        - fasta_io: Read and write FASTA format.
        - genbank_io: Read GenBank flat files.
        - intelligenetics_io: Read IntelliGenetics format.
        - msf_io: Read sequence information in MSF format.
        - nbrf_io: Sequence IO for NBRF/PIR format.
        - nexus_io: Read the sequence data from a nexus file.
        - null_io: Null sequence IO.
        - phylip_io: Read Sequences in interleaved Phylip format.
        - plain_io: Read and write raw, unformatted sequence data.
        - stockholm_io: Read a STOCKHOLM format.
        - table_io: Read  tab delimited format.
    - ssearch_io: Parse sequence search analysis reports.
        - blastxml: Read BLAST XML output.
        - fasta: Read the output of a fasta similarity search.
    - transform: Transformations of Seqs (alphabetic sequences),
            including translation with a full suite of
Gavin Crooks and John Gilman

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