Team:TU-Munich/Results/Software

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Revision as of 00:17, 10 July 2013


The AutoAnnotator

Introduction to the Idea behind our AutoAnnotator

The parts registry contains a wide range of interesting BioBricks from which many have similarity: they are not perfectly described and annotated. This is a real pity because after the identification of the open reading fram a multitude of parameters of the protein can be computed automatically. We are developing a tool which is able to identify the open reading frame of a BioBrick, analyze it for different parameters and export the results in a format that can easily be importet into a part description a a single table.
Figure on the steps.

Import of BioBrick Sequences

Text
figure




Determination of the Open Reading Frame

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figure




Analysis of Parameters

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figure




Export of the Computed Parameters

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figure


Automatically determined parameters using the [http://www.mediawiki.org/wiki/Table BioBrick-AutoAnnotator]
BioBrick: <partinfo>BBa_K1159000</partinfo> Used open reading frame from position ?x? to ?y?.
A (Ala) ?4 R (Arg) ?4 N (Asn) ?4 D (Asp) ?4? C (Cys) ?4 Q (Gln) ?4 E (Glu) ?4 G (Gly) ?4 H (His) ?4?
K (Lys): ?4 M (Met) ?4 F (Phe) ?4 P (Pro) ?4 S (Ser) ?4 T (Thr) ?4 W (Trp) ?4 Y (Tyr) ?4 V (Val) ?4
Amino acid counting: Total number of amino acids (aa): ?99? Number of positively charged aa: ?9? Number of negatively charged aa: ?9?
Biochemical parameters: Molecular weight [Da]: ?4? Theoretical pI: ?4? Extinction coefficient: ?4?
Estimated half-life: Mammals: ?4 h? Yeast: ?4? E. coli: ?4?
Codon usage: Mammals: ?good? Yeast: ?Ok? E. coli: ?bad ?
The BioBrick-AutoAnnotator was created by TU-Munich 2013 iGEM team. For information please read the description.



References:

http://www.ncbi.nlm.nih.gov/pubmed/6327079 Edens et al., 1984

  1. http://www.ncbi.nlm.nih.gov/pubmed/6327079 Edens et al., 1984 Edens, L., Bom, I., Ledeboer, A. M., Maat, J., Toonen, M. Y., Visser, C., and Verrips, C. T. (1984). Synthesis and processing of the plant protein thaumatin in yeast. Cell, 37(2):629–33.



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