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Team:Johns Hopkins-Software/Compatibility
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Overview | Overview | ||
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| - | When creating Autogene, we acknowledged the various different DNA file formats. We knew that <a href="http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord">Genbank </a>, which is the common file format used to store genetic data in the National Center of Biotechnology Information would be one of the most used file formats to obtain genetic sequences. We also took into account <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml">FASTA</a> formats, and the new standard for documentation, <a href="http://www.sbolstandard.org/initiatives/serialization">SBOL </a>. | + | When creating Autogene, we acknowledged the various different DNA file formats. We knew that <a href="http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord">Genbank</a>, which is the common file format used to store genetic data in the National Center of Biotechnology Information, would be one of the most used file formats to obtain genetic sequences. We also took into account <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml">FASTA</a> formats, and the new standard for synthetic biology documentation, <a href="http://www.sbolstandard.org/initiatives/serialization">SBOL</a>. |
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| - | Autogene is capable of importing and exporting genetic sequences in the following file formats:<br> | + | Using biojava and libSBOLj libraries, Autogene is capable of importing and exporting genetic sequences in the following file formats:<br> |
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| - | + | <li>FASTA</li> | |
| - | + | <li>Genbank</li> | |
| + | <li>SBOL</li> | ||
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*The genbank files Autogene can import/export are also ApE compatible. <a href="http://biologylabs.utah.edu/jorgensen/wayned/ape/">ApE </a> (A plasmid Editor) is a synthetic biology tool that outputs files in a unique genbank format that contains information on annotation color. | *The genbank files Autogene can import/export are also ApE compatible. <a href="http://biologylabs.utah.edu/jorgensen/wayned/ape/">ApE </a> (A plasmid Editor) is a synthetic biology tool that outputs files in a unique genbank format that contains information on annotation color. | ||
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| + | Future Work | ||
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| + | We plan on increasing the amount of file options for Autogene, such as GFF3, Embl, and DDBJ. | ||
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