This project aimed to find a method for producing potential probe targets for identification of ESBL (Extended Spectrum Beta Lactamase) genes in bacteria. ESBLs are a type of enzymes responsible for antibiotic resistance in many bacteria. The result we developed was a semi-automated pipeline that utilises several Perl scripts to download gene sequences, identify sequence subgroups based on sequence similarity, find common target sequences among them and screen the target sequences against a background database. These target sequences should work with padlock probes and therefore had specific requirements regarding length and highest number of allowed mismatches. This report includes descriptions of the scripts and ideas for future improvements, as well as an ethical analysis about aspects relevant to research on antibiotic resistance.
| Identifer | oai:union.ndltd.org:UPSALLA1/oai:DiVA.org:uu-323686 |
| Date | January 2017 |
| Creators | Haughey, Caitlin, Mesilaakso, Lauri, Berner-Wik, Erik, Östlund, Emma, Ulfsparre, Jonatan, Olin, Hampus |
| Publisher | Uppsala universitet, Institutionen för biologisk grundutbildning, Uppsala universitet, Institutionen för biologisk grundutbildning, Uppsala universitet, Institutionen för biologisk grundutbildning, Uppsala universitet, Institutionen för biologisk grundutbildning, Uppsala universitet, Institutionen för biologisk grundutbildning, Uppsala universitet, Institutionen för biologisk grundutbildning |
| Source Sets | DiVA Archive at Upsalla University |
| Language | English |
| Detected Language | English |
| Type | Student thesis, info:eu-repo/semantics/bachelorThesis, text |
| Format | application/pdf |
| Rights | info:eu-repo/semantics/openAccess |
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