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Team:UPO-Sevilla/Project/Notebook/Bioinformatics
From 2011.igem.org
Notebook
Bioinformatics
Aida Moreno
Week 1
Week 2
Week 3
Week 4
Week 5
Week 6
Week 7
Week 8
Week 9
Week 10
Week 11
Bioinformatics brain storming week: During this fist summer week of work, during the summer, I asked wet labs colleagues about their needs and ideas with the aim of making (to make) a list of useful bioinformatics analyses.
I also worked in the development of a Perl program to meet the need of the V sublab of searching on E.coli's proteome, before starting their wet work.
I met with my supervisor (Antonio J. Pérez) and we worked in selecting what ideas, from the wet labs’, were more interesting. Moreover, we decided to perform other parallel studies which could be helpful, always keeping in mind the two-months time we had before the European Jamboree.
I also started a bibliographic research to check all the reported information which was related to the issues we were determined to work on.
Understanding the Tn7 system. I downloaded sequences and looked for useful software to start getting results. I found several problems when downloading genetic sequences and managing them. My supervisor helped me to deal with all genetic databases in an efficient way.
Once, several multi sequence alignments were done, I started with all the project dockings. I ran a lot of them and I selected the best results. Before running all dockings, I needed pdf files of all the proteins under study so I had to run lots of times a homology modelling server. I ended up with a bunch of results which I analysed before starting to perform dockings. I asked my supervisor for help on how to deal with so many results.
I chose a molecule viewer and learned how to use the command line. At first, I started working with RasMol viewer but I changed to Jmol due to the fact that RasMol lacked some functions.
Firsts contact with our dockings pdb files.
I have been working all week long with attTn7 analyses. When I found a problem I would just consider it since I had other priorities such us getting a RNA secondary structure and improving the Perl initial written program.
I looked for other software different from TreeView to perform phylogenetic trees. I found several useful ones and I tried them all. I also looked for a platform to calculate logos. At the end of the week I ended up with trees and logos for all the alignments which I already had.
I went to wet labs to keep them up-to-date about all my work. I also asked them for more ideas. The rest of the week I worked on getting all the results from the Tn7 system.
During this week I finished all the structure-related analyses and I discussed the results with Antonio J. Pérez. We also had a group meeting, with all the members, in which we presented all the results and based on this, the group gave us some new interesting ideas.
Getting the last results and deciding which information is worthless. Writing and presenting all our work. Difficult task to achieve due to the huge amount of data we have!!
Hard work time, packaging everything to upload it to our wiki. Done with it!! :D:D
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