Team:TU-Munich/Results/Software

From 2013.igem.org

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Revision as of 23:03, 7 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.

Import of BioBrick Sequences

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Determination of the Open Reading Frame

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Analysis of Parameters

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Export of the Computed Parameters

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Automatically determined parameters using the [http://www.mediawiki.org/wiki/Table BioBrick-AutoAnnotator]

BioBrick Nr.:

?BBa_?

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 coefficients:

?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

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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 <!-- Start of content -->
-==The AutoAnnotater==
+==The AutoAnnotator==
 ===Introduction to the Idea behind our AutoAnnotator===
 <div class="box-center">

Team:TU-Munich/Results/Software

From 2013.igem.org

Revision as of 23:03, 7 July 2013

The AutoAnnotator

Introduction to the Idea behind our AutoAnnotator

Import of BioBrick Sequences

Determination of the Open Reading Frame

Analysis of Parameters

Export of the Computed Parameters

References:

AutoAnnotator:

Follow us:

Address: