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Team:Johns Hopkins-Software/PathogenDetection
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| - | <div id="project_temp"><div id="title">Pathogen Detection Using Autogene</div> | + | <div id="project_temp">For our Human Practices component, we conducted BioBrick analysis using our software tools. Firstly, we created genbank files of each BioBrick with annotations generated from the Autogene database of features and found using our alignment software, and secondly, we searched the BioBrick repository for pathogenic sequences.<br><br><div id="title">BioBrick Analysis</div><br>Using Autogene's feature database and alignment software, we annotated the BioBricks in the repository. We are still in the process of creating the genbank files, but they will be available <a href = "http://ugrad.cs.jhu.edu/~escher1/autogene/genbank_files.html">here</a> when they are produced.<br><br><p>Using Autogene’s feature database and alignment algorithms, we also did some preliminary cross-analysis of our annotations with those provided by the Registry of Standard Biological Parts for 10 biobrick parts. We noticed that there were a few differences between our annotations, and the ones provided. |
| + | A listing of the key differences can be found <a href = "http://ugrad.cs.jhu.edu/~escher1/autogene/biobrick_annotations.html">here</a>. | ||
| + | </p> | ||
| + | <br><div id="title">Pathogen Detection Using Autogene</div><br> | ||
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As biological research becomes easier and easier with the development of new tools and increased understanding, | As biological research becomes easier and easier with the development of new tools and increased understanding, | ||
there is also increased danger. Not only are many pathogen sequences freely available on the internet, but the DNA production process has become so simple and well understood, that any amateur biologist or hobbyist now has the ability to synthesize their own sequences. While in some ways this can be positive, the this also poses a clear threat, and exemplifies a need for an increase in pathogen detection tools. | there is also increased danger. Not only are many pathogen sequences freely available on the internet, but the DNA production process has become so simple and well understood, that any amateur biologist or hobbyist now has the ability to synthesize their own sequences. While in some ways this can be positive, the this also poses a clear threat, and exemplifies a need for an increase in pathogen detection tools. | ||
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Most oligo production companies now screen their orders for pathogen sequences, but there are many online resources that have yet to be analyzed, including the BioBrick repository. For this reason, we decided to use our new software tools to search for pathogen sequences in the basic BioBrick sequences (defined as those under 1000 bases in length). People all over the world contribute to the BioBrick registry, and there is no algorithmic validation of their annotations, or of the safety of the uploaded features. As thousands of people use these sequences, this poses a great threat as, if a pathogenic sequence were uploaded, many people could be exposed to dangerous pathogens if the sequence were ever produced. | Most oligo production companies now screen their orders for pathogen sequences, but there are many online resources that have yet to be analyzed, including the BioBrick repository. For this reason, we decided to use our new software tools to search for pathogen sequences in the basic BioBrick sequences (defined as those under 1000 bases in length). People all over the world contribute to the BioBrick registry, and there is no algorithmic validation of their annotations, or of the safety of the uploaded features. As thousands of people use these sequences, this poses a great threat as, if a pathogenic sequence were uploaded, many people could be exposed to dangerous pathogens if the sequence were ever produced. | ||
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| - | We used our software to search over | + | We used our software to search over <font style="BACKGROUND-COLOR: #ffff66">11,000</font> BioBricks for over <font style="BACKGROUND-COLOR:#ffff66">2,500</font> pathogen sequences, using DNA-based, Smith-Waterman alignments. While we did not find any matches in this subset of the BioBrick parts, we hope to continue our analysis on both these parts, and the rest of the registry, by using Amino Acid alignments. |
It is important to establish protocols of this nature for pathogen detection in large databases of sequences. Before DNA is produced, it is necessary to establish that it does not pose a threat to those who are producing it, or to anyone else who could be exposed. | It is important to establish protocols of this nature for pathogen detection in large databases of sequences. Before DNA is produced, it is necessary to establish that it does not pose a threat to those who are producing it, or to anyone else who could be exposed. | ||
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<br><br> | <br><br> | ||
| - | + | This analysis is ongoing, but here are the BioBricks we have already analyzed:<br><br> | |
| - | <table></tr><tr> | + | <center><table></tr><tr> |
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BBa_K299006 | BBa_K299006 | ||
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BBa_Z52934 | BBa_Z52934 | ||
| - | </td></tr></table> | + | </td></tr></table></center> |
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{{:Team:Johns_Hopkins-Software/header}} | {{:Team:Johns_Hopkins-Software/header}} | ||
