Poster Meeting

“The whole life of a man is but a point in time; let us enjoy it, Plutarch”

We finally meet all together !!!

(In the meanwhile I was studying for the exam of Applied Gene Technology) We have already started working on the poster preparation, but we wanted to try some things regarding the inverted repeats and the gc content.

Regarding the inverted repeats we tried to use different databases as:

• REPuter - fast computation of maximal repeats in complete genomes (S. Kurtz & C. Scheiermacher @ Universitat Bielefeld, Germany) - interesting graphical representation of repeats
• REPFIND (ZLAB, Dr. Zhiping Weng, Boston University, U.S.A.) - on sequences of less than 20kb it provides graphical and statistical analysis on direct repeats.
• einverted, - (EMBOSS) - find inverted and tandem repeats

(documentation: http://molbiol-tools.ca/Repeats_secondary_structure_Tm.htm)

We concluded by using EMBOSS einverted cause it was most user friendly and practically we could interpret better the results! We concluded that there were 14 inverted repeats with 4 of them having 100% identity and the longest of these being 20bp. We were thinking firstly that we should have found only 1 inverted repeat. Also in the REPuter it seemed that there were more inverted repeats. Probably those differences are due to the different algorithms that various databases use.

At the same time I have started from the previous night to try to calculate the gc content! I tried to do that through uppmax by using EMBOSS, but my results were unreadable!! I tried then to run locally, through the main database of EMBOSS: http://www.bioinformatics.nl/cgi-bin/emboss/geecee

The file I used was: chloro-scaffolds.fa The results look like that:

X.Sequence	GC.conent
1	0.47
2	0.41
3	0.38
4	0.47
6	0.43
7	0.66
9	0.48
10	0.50
11	0.40
12	0.41
15	0.45
17	0.36
18	0.56
20	0.45
21	0.44
22	0.48
26	0.25
28	0.32
29	0.50
30	0.39
31	0.36

We finished the poster and we sent the email to be printed in A1 format.