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UGent - BCCM/LMBP Plasmidencollectie
Voorstel stage bio-informatica (2017-18): Implementation of new search functions for the BCCM/GeneCorner online database to find plasmids based on specific biological properties and functions
- Genereren van verschillende output formaten zoals EMBL en GenBank.
- Genereren van een grafische map.
- Genereren van de complementaire sequentie.
- De databank uitbreiden met nieuwe features:
- De mogelijkheid voorzien waarbij gebruikers eigen features kunnen opladen.
- Voorzien van keuzemogelijkheden wat er dient opgenomen te worden in de te genereren bestanden zoals:
- Voorzien van automatische updates waarbij alle input databanken bvb. wekelijks gescreend worden op nieuwe features.
- Aanduiden van open reading frames (ORFs) die bvb. minstens 200 codons groot zijn (zelf aan te passen), welke dan kunnen vertaald worden naar hun eiwit sequentie (met aanduiding van bepaalde domeinen en actieve sites en omzetting naar een 3D structuur).
- Opsporen van relevante restrictiepatronen: het zoeken van optimale digesten waardoor bvb. 2 of 3 fragmenten van welbepaalde lengtes ontstaan.
- Het zoeken van sequencing primers.
- Het maken van een tutorial voor de applicatie.
- Voorzien van blast mogelijkheden, bvb tegen de EMBL databank
Abstract traineeship advanced bachelor of bioinformatics (2017-18): Implementation of new search functions for the BCCM/GeneCorner online database to find plasmids based on specific biological properties and functions
The purpose of this research was to write a script that will implement a new search function for the BCCM/GeneCorner online database to find plasmids based on specific biological properties and functions. I used PHP as programming language and a PostgreSQL database containing the BCCM/GeneCorner plasmid collection.
The BCCM/GeneCorner Plasmid Collection provides services that accepts and distributes plasmids to researchers worldwide. The BCCM/GeneCorner is a non-profit consortium funded by the Belgian Science Policy (Belspo) which has evolved to a unique plasmid repository in Europe. The consortium exists of seven complementary and research-based culture collections of authenticated biological material and it is embedded in the Department of Biomedical Molecular Biology and the VIB-UGent Center for Inflammation Research.
BCCM/GeneCorner is continuously improving their online catalogue of plasmids with the aim of making the online catalogues user friendly. My project will enable clients to search on gene ontology terms, interaction or pathways. It will also help to generate the associated plasmid containing the gene(s) related with these terms. In this way the client will retrieve plasmids that suits their needs more easily.
My script retrieves automatically the corresponding gene ontology terms, interactions and pathways of the genes found in the public available plasmids from NCBI. Therefore, the public plasmids need to be linked to one or more Gene IDs. The available public plasmids as well as the public library clones (human ORF clones and shRNA clones) are added to the results. The BCCM IT team will implement the search function in the online plasmid catalogue which will retrieve a list of plasmids from the BCCM/GeneCorner Plasmid Collection. The possible search criteria’s of this service are a gene ontology term, pathway or interaction. But there is also the possibility to enter a gene name or gene symbol after having selected a pathway, an interaction or a gene ontology term.
Tags: bioinformatics |
Address
Technologiepark 927
Gent
Tel1: +32 9 33 13 843 Tel2: +32 9 33 13 600 Belgium |
Contacts
Traineeship supervisor
Prof. Dr. Rudi Beyaert
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Traineeship supervisor
Martine Vanhoucke
martine.vanhoucke@ugent.be |