Team:TU-Munich/Results/Software

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(Difference between revisions)
(→Export of the Computed Parameters)
(→Export of the Computed Parameters)
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{|cellspacing="0" border="1"
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{|cellspacing="0" border="1"  
|colspan="20"|'''Automatically determined parameters using the [http://www.mediawiki.org/wiki/Table BioBrick-AutoAnnotator]'''
|colspan="20"|'''Automatically determined parameters using the [http://www.mediawiki.org/wiki/Table BioBrick-AutoAnnotator]'''
|-
|-
-
|colspan="10"|BioBrick: <partinfo>BBa_K1159000</partinfo>
+
|colspan="20"|'''Nucleotide sequence:''' (underlined part was translated, italic parts were added)<br>GTACACA<u>ATGCGTCGT...TTCGAAAAA</u>TAA
-
|colspan="10"|Used open reading frame from position ?x? to ?y?.
+
|-
|-
-
|A (Ala)
+
|colspan="20"|'''Amino acid sequence:'''<br>MRRSANYQPSIWDHDFLQSLNSNYTDEAYKRRAEELRGKVKIAIKDVIEPLDQLDLIDNLQRLGLAHRFETEIRNILNNIYNNNKDYNWRKENLYATSLEFRLLRQHGYPVSQEVFNGFKDDQGGFICDDFKGILSLHEASYYSLEGESIMEEAWQFTSKHLKEVMISKNMEEDVFVAEQAKRALELPLHWKVPMLEARWFIHIYERREDKNHLLLELAKMEFNTLQAIYQEELKEISGWWKDTGLGEKLSFARNRLVASFLWSMGIAFEPQFAYCRRVLTISIALITVIDDIYDVYGTLDELEIFTDAVERWDINYALKHLPGYMKMCFLALYNFVNEFAYYVLKQQDFDLLLSIKNAWLGLIQAYLVEAKWYHSKYTPKLEEYLENGLVSITGPLIITISYLSGTNPIIKKELEFLESNPDIVHWSSKIFRLQDDLGTSSDEIQRGDVPKSIQCYMHETGASEEVARQHIKDMMRQMWKKVNAYTADKDSPLTGTTTEFLLNLVRMSHFMYLHGDGHGVQNQETIDVGFTLLFQPIPLEDKHMAFTASPGTKGTGAWSHPQFEK
-
|?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):
+
|colspan="10"|BioBrick: <partinfo>BBa_K801060</partinfo>
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|?4
+
|colspan="10"|Used open reading frame from position 8 to 1705 (excluding stop-codon; if appropriate prefix/suffix were added).
-
|M (Met)
+
-
|?4
+
-
|F (Phe)
+
-
|?4
+
-
|P (Pro)
+
-
|?4
+
-
|S (Ser)
+
-
|?4
+
-
|T (Thr)
+
-
|?4
+
-
|W (Trp)
+
-
|?4
+
-
|Y (Tyr)
+
-
|?4
+
-
|V (Val)
+
-
|?4
+
|-
|-
-
|colspan="3"|'''Amino acid counting:'''
+
|colspan="2"|A (Ala)
-
|colspan="3"|Total number of amino acids (aa):
+
|colspan="2"|33 (5.83%)
-
|colspan="2"|?99?
+
|colspan="2"|R (Arg)
-
|colspan="3"|Number of positively charged aa:
+
|colspan="2"|25 (4.42%)
-
|colspan="2"|?9?
+
|colspan="2"|N (Asn)
-
|colspan="3"|Number of negatively charged aa:
+
|colspan="2"|27 (4.77%)
-
|colspan="2"|?9?
+
|colspan="2"|D (Asp)
 +
|colspan="2"|34 (6.01%)
 +
|colspan="2"|C (Cys)
 +
|colspan="2"|4 (0.71%)
|-
|-
-
|colspan="3"|'''Biochemical parameters:'''
+
|colspan="2"|Q (Gln)
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|colspan="3"|Molecular weight [Da]:
+
|colspan="2"|24 (4.24%)
-
|colspan="2"|?4?
+
|colspan="2"|E (Glu)
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|colspan="3"|Theoretical pI:
+
|colspan="2"|48 (8.48%)
-
|colspan="2"|?4?
+
|colspan="2"|G (Gly)
-
|colspan="3"|Extinction coefficient:
+
|colspan="2"|29 (5.12%)
-
|colspan="2"|?4?
+
|colspan="2"|H (His)
 +
|colspan="2"|18 (3.18%)
 +
|colspan="2"|I (Ile)
 +
|colspan="2"|39 (6.89%)
|-
|-
-
|colspan="3"|'''Estimated half-life:'''
+
|colspan="2"|L (Leu)
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|colspan="3"|Mammals:
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|colspan="2"|64 (11.31%)
-
|colspan="2"|?4 h?
+
|colspan="2"|K (Lys)
-
|colspan="3"|Yeast:
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|colspan="2"|36 (6.36%)
-
|colspan="2"|?4?
+
|colspan="2"|M (Met)
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|colspan="3"|''E. coli'':
+
|colspan="2"|16 (2.83%)
-
|colspan="2"|?4?
+
|colspan="2"|F (Phe)
 +
|colspan="2"|28 (4.95%)
 +
|colspan="2"|P (Pro)
 +
|colspan="2"|17 (3.00%)
|-
|-
-
|colspan="3"|'''Codon usage:'''
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|colspan="2"|S (Ser)
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|colspan="3"|Mammals:
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|colspan="2"|33 (5.83%)
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|colspan="2"|?good?
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|colspan="2"|T (Thr)
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|colspan="3"|Yeast:
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|colspan="2"|26 (4.59%)
-
|colspan="2"|?Ok?
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|colspan="2"|W (Trp)
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|colspan="3"|''E. coli'':
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|colspan="2"|14 (2.47%)
-
|colspan="2"|?bad ?
+
|colspan="2"|Y (Tyr)
 +
|colspan="2"|27 (4.77%)
 +
|colspan="2"|V (Val)
 +
|colspan="2"|24 (4.24%)
|-
|-
-
|colspan="3"|'''RFC standard:'''
+
|colspan="2"|'''Amino acid counting:'''
-
|colspan="17"|This is a RFC 25 BioBrick, thus ATGGCCGGC and ACCGGT were added to the 5' and 3' ends.
+
|colspan="4"|Total number of amino acids (aa):
 +
|colspan="2"|566
 +
|colspan="4"|Number of positively charged aa (Arg + Lys):
 +
|colspan="2"|61
 +
|colspan="4"|Number of negatively charged aa (Asp + Glu):
 +
|colspan="2"|82
|-
|-
-
|colspan="20"|AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
|colspan="2"|'''Biochemical parameters:'''
 +
|colspan="4"|Molecular weight [Da]:
 +
|colspan="2"|66105.33
 +
|colspan="4"|Theoretical pI:
 +
|colspan="2"|5.38
 +
|colspan="4"|Extinction coefficient: [M^-1 cm^-1]
 +
|colspan="2"|117480 (all Cys as cystine), 117230 (no Cys as cystine)
 +
|-
 +
|colspan="2"|'''Estimated half-life:'''
 +
|colspan="4"|Mammals:
 +
|colspan="2"|30 hour
 +
|colspan="4"|Yeast:
 +
|colspan="2"|>20 hour
 +
|colspan="4"|''E. coli'':
 +
|colspan="2"|>10 hour
 +
|-
 +
|colspan="2"|'''Codon usage:''' (CAI)
 +
|colspan="4"|Mammals:
 +
|colspan="2"|0.68
 +
|colspan="4"|Yeast:
 +
|colspan="2"|0.69
 +
|colspan="4"|''E. coli'':
 +
|colspan="2"|0.71
 +
|-
 +
|colspan="3"|'''RFC standard:'''
 +
|colspan="17"|This is a RFC 10 BioBrick, nothing was added
|-
|-
-
|colspan="20"| The BioBrick-AutoAnnotator was created by [https://2013.igem.org/Team:TU-Munich TU-Munich 2013] iGEM team. Software License??? For information please read the [https://2013.igem.org/Team:TU-Munich/Results/Software description].
+
|colspan="20"| The BioBrick-AutoAnnotator was created by [https://2013.igem.org/Team:TU-Munich TU-Munich 2013] iGEM team. For information please read the [https://2013.igem.org/Team:TU-Munich/Results/Software description].
|}
|}
 +
<br><br>
<br><br>

Revision as of 14:43, 26 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

Text
figure




Analysis of Parameters

Text
figure




Export of the Computed Parameters

Text


figure


Automatically determined parameters using the [http://www.mediawiki.org/wiki/Table BioBrick-AutoAnnotator]
Nucleotide sequence: (underlined part was translated, italic parts were added)
GTACACAATGCGTCGT...TTCGAAAAATAA
Amino acid sequence:
MRRSANYQPSIWDHDFLQSLNSNYTDEAYKRRAEELRGKVKIAIKDVIEPLDQLDLIDNLQRLGLAHRFETEIRNILNNIYNNNKDYNWRKENLYATSLEFRLLRQHGYPVSQEVFNGFKDDQGGFICDDFKGILSLHEASYYSLEGESIMEEAWQFTSKHLKEVMISKNMEEDVFVAEQAKRALELPLHWKVPMLEARWFIHIYERREDKNHLLLELAKMEFNTLQAIYQEELKEISGWWKDTGLGEKLSFARNRLVASFLWSMGIAFEPQFAYCRRVLTISIALITVIDDIYDVYGTLDELEIFTDAVERWDINYALKHLPGYMKMCFLALYNFVNEFAYYVLKQQDFDLLLSIKNAWLGLIQAYLVEAKWYHSKYTPKLEEYLENGLVSITGPLIITISYLSGTNPIIKKELEFLESNPDIVHWSSKIFRLQDDLGTSSDEIQRGDVPKSIQCYMHETGASEEVARQHIKDMMRQMWKKVNAYTADKDSPLTGTTTEFLLNLVRMSHFMYLHGDGHGVQNQETIDVGFTLLFQPIPLEDKHMAFTASPGTKGTGAWSHPQFEK
BioBrick: <partinfo>BBa_K801060</partinfo> Used open reading frame from position 8 to 1705 (excluding stop-codon; if appropriate prefix/suffix were added).
A (Ala) 33 (5.83%) R (Arg) 25 (4.42%) N (Asn) 27 (4.77%) D (Asp) 34 (6.01%) C (Cys) 4 (0.71%)
Q (Gln) 24 (4.24%) E (Glu) 48 (8.48%) G (Gly) 29 (5.12%) H (His) 18 (3.18%) I (Ile) 39 (6.89%)
L (Leu) 64 (11.31%) K (Lys) 36 (6.36%) M (Met) 16 (2.83%) F (Phe) 28 (4.95%) P (Pro) 17 (3.00%)
S (Ser) 33 (5.83%) T (Thr) 26 (4.59%) W (Trp) 14 (2.47%) Y (Tyr) 27 (4.77%) V (Val) 24 (4.24%)
Amino acid counting: Total number of amino acids (aa): 566 Number of positively charged aa (Arg + Lys): 61 Number of negatively charged aa (Asp + Glu): 82
Biochemical parameters: Molecular weight [Da]: 66105.33 Theoretical pI: 5.38 Extinction coefficient: [M^-1 cm^-1] 117480 (all Cys as cystine), 117230 (no Cys as cystine)
Estimated half-life: Mammals: 30 hour Yeast: >20 hour E. coli: >10 hour
Codon usage: (CAI) Mammals: 0.68 Yeast: 0.69 E. coli: 0.71
RFC standard: This is a RFC 10 BioBrick, nothing was added
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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       $members.eq(i).addClass("right");

   } else if ( ( $members.eq(i).offset().top + $members.eq(i).height() ) < event.pageY ) {

       $members.eq(i).removeClass();
       $members.eq(i).addClass("bottom-right");

   }

}

} });

}

});

Retrieved from "http://2013.igem.org/Team:TU-Munich/Results/Software"