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https://img.shields.io/pypi/pyversions/biotite.svg\n   :alt: Python version\n.. image:: https://github.com/biotite-dev/biotite/actions/workflows/test_and_deploy.yml/badge.svg\n   :target: https://github.com/biotite-dev/biotite/actions/workflows/test_and_deploy.yml\n   :alt: Test status\n\n.. image:: https://www.biotite-python.org/_static/assets/general/biotite_logo_m.png\n   :alt: The Biotite Project\n\nBiotite project\n===============\n\n*Biotite* is your Swiss army knife for bioinformatics.\nWhether you want to identify homologous sequence regions in a protein family\nor you would like to find disulfide bonds in a protein structure: *Biotite*\nhas the right tool for you.\nThis package bundles popular tasks in computational molecular biology\ninto a uniform *Python* library.\nIt can handle a major part of the typical workflow\nfor sequence and biomolecular structure data:\n\n   - Searching and fetching data from biological databases\n   - Reading and writing popular sequence/structure file formats\n   - Analyzing and editing sequence/structure data\n   - Visualizing sequence/structure data\n   - Interfacing external applications for further analysis\n\n*Biotite* internally stores most of the data as *NumPy* `ndarray` objects,\nenabling\n\n   - fast C-accelerated analysis,\n   - intuitive usability through *NumPy*-like indexing syntax,\n   - extensibility through direct access of the internal *NumPy* arrays.\n\nAs a result the user can skip writing code for basic functionality (like\nfile parsers) and can focus on what their code makes unique - from\nsmall analysis scripts to entire bioinformatics software packages.\n\nIf you use *Biotite* in a scientific publication, please cite:\n\n| Kunzmann, P. \u0026 Hamacher, K. BMC Bioinformatics (2018) 19:346.\n| `\u003chttps://doi.org/10.1186/s12859-018-2367-z\u003e`_\n\n\nInstallation\n------------\n\n*Biotite* requires the following packages:\n\n   - **numpy**\n   - **requests**\n   - **msgpack**\n   - **networkx**\n\nSome functions require some extra packages:\n\n   - **matplotlib** - Required for plotting purposes.\n\n*Biotite* can be installed via *Conda*...\n\n.. code-block:: console\n\n   $ conda install -c conda-forge biotite\n\n... or *pip*\n\n.. code-block:: console\n\n   $ pip install biotite\n\n\nUsage\n-----\n\nHere is a small example that downloads two protein sequences from the\n*NCBI Entrez* database and aligns them:\n\n.. code-block:: python\n\n   import biotite.sequence.align as align\n   import biotite.sequence.io.fasta as fasta\n   import biotite.database.entrez as entrez\n\n   # Download FASTA file for the sequences of avidin and streptavidin\n   file_name = entrez.fetch_single_file(\n       uids=[\"CAC34569\", \"ACL82594\"], file_name=\"sequences.fasta\",\n       db_name=\"protein\", ret_type=\"fasta\"\n   )\n\n   # Parse the downloaded FASTA file\n   # and create 'ProteinSequence' objects from it\n   fasta_file = fasta.FastaFile.read(file_name)\n   avidin_seq, streptavidin_seq = fasta.get_sequences(fasta_file).values()\n\n   # Align sequences using the BLOSUM62 matrix with affine gap penalty\n   matrix = align.SubstitutionMatrix.std_protein_matrix()\n   alignments = align.align_optimal(\n       avidin_seq, streptavidin_seq, matrix,\n       gap_penalty=(-10, -1), terminal_penalty=False\n   )\n   print(alignments[0])\n\n.. code-block::\n\n   MVHATSPLLLLLLLSLALVAPGLSAR------KCSLTGKWDNDLGSNMTIGAVNSKGEFTGTYTTAV-TA\n   -------------------DPSKESKAQAAVAEAGITGTWYNQLGSTFIVTA-NPDGSLTGTYESAVGNA\n\n   TSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFS----ESTTVFTGQCFIDRNGKEV-LKTMWLLRSSVN\n   ESRYVLTGRYDSTPATDGSGT--ALGWTVAWKNNYRNAHSATTWSGQYV---GGAEARINTQWLLTSGTT\n\n   DIGDDWKATRVGINIFTRLRTQKE---------------------\n   -AANAWKSTLVGHDTFTKVKPSAASIDAAKKAGVNNGNPLDAVQQ\n\nMore documentation, including a tutorial, an example gallery and the API\nreference is available at `\u003chttps://www.biotite-python.org/\u003e`_.\n\n\nContribution\n------------\n\nInterested in improving *Biotite*?\nHave a look at the\n`contribution guidelines \u003chttps://www.biotite-python.org/latest/contribution/index.html\u003e`_.\nFeel free to join our community chat on `Discord \u003chttps://discord.gg/cUjDguF\u003e`_.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiotite-dev%2Fbiotite","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiotite-dev%2Fbiotite","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiotite-dev%2Fbiotite/lists"}