Team:TU-Munich/Results/Software

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The AutoAnnotator

Introduction to the Idea behind our AutoAnnotator

Figure 1:

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

Text

<partinfo>BBa_K801060</partinfo>



Determination of the Open Reading Frame

Text




Computation of Parameters

Text


Molecular weight

Theoretical pI

Extinction coefficient at 280 nm

Estimated half-life

Codon usage (CAI)



Export of the Computed Parameters

Text


Example for the table created for a popular BioBrick

BioBrick: BBa_E0040Automatically determined parameters using the BioBrick-AutoAnnotator version 1.0
RFC standard:RFC 10 BioBrick, nothing was addedORF from 1 to 714 (excluding stop-codon)
Nucleotide sequence: (underlined part encodes the protein, italic parts were added)
 ATGCGTAAA ... CTATACAAATAATAA
Amino acid sequence:
  1 MRKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFGYGVQCFARYPDHMKQHDFFKSAMPEGYVQERTIFF
101 KDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHY
201 LSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK
Amino acid composition:
A (Ala)9 (3.8%)C (Cys)2 (0.8%)H (His)10 (4.2%)M (Met)6 (2.5%)T (Thr)15 (6.3%)
R (Arg)7 (2.9%)Q (Gln)8 (3.4%)I (Ile)12 (5.0%)F (Phe)13 (5.5%)W (Trp)1 (0.4%)
N (Asn)13 (5.5%)E (Glu)16 (6.7%)L (Leu)19 (8.0%)P (Pro)10 (4.2%)Y (Tyr)11 (4.6%)
D (Asp)18 (7.6%)G (Gly)23 (9.7%)K (Lys)20 (8.4%)S (Ser)8 (3.4%)V (Val)17 (7.1%)
Amino acid counting:Total number of amino acids (aa):238Positively charged aa (Arg + Lys):27Negatively charged aa (Asp + Glu):34
Biochemical parameters:Molecular weight [Da]:26909.4Theoretical pI:5.8Extinction coefficient at 280 nm [M-1 cm-1]:22015 (all Cys as cystine)
21890 (all Cys reduced)
Estimated half-life [h]:E. coli:>10S. cervisiae:>20Mammals:30
Codon usage (CAI):E. coli:0.72S. cervisiae:0.75Mammals:0.68
The BioBrick-AutoAnnotator was created by TU-Munich 2013 iGEM team. For information please read the description.


How to use the BioBrick-AutoAnnotator

During some late nights, we have ...

Source code of the BioBrick-Autoannotator

source code




Application of our Software-tool

Annotation by TU-Munich 2013 Team

Annotation by other Teams



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 prossing of the plant protein thaumatin in yeast. Cell, 37(2):629–33.
  2. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC340524/ Sharp and Li, 1987 Sharp, P.M. and Li, W.H. (1987). The codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications. "Nucleic Acids Res.", 15(3):1281–95.
  3. http://onlinelibrary.wiley.com/store/10.1046/j.1365-2443.1997.1020301.x/asset/j.1365-2443.1997.1020301.x.pdf?v=1&t=hjneqjmt&s=c6badbf62c94c8e3417d62c4bad750ba930dbdae Varshavsky, 1997 Varshavsky, A. (1997). The N-end rule pathway of protein degradation. "Genes to Cells", 2:13 – 28.
  4. http://www.ncbi.nlm.nih.gov/pubmed/2506181 Varshavsky et al., 1989 Varshavsky, A., Gonda, D.K., Bachmair, A., Wünning, I., Tobias, J.W. and Lane, W.S. (1989). Universality and structure of the N-end rule. "J. Biol. Chem.", 264(28):16700-12.




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