Team:Goettingen/Project/Bioinformatical Tools

From 2012.igem.org

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{{GoettingenHeader|deu=Team:Goettingen/Project/Bioinformatical Tools|eng=Team:Goettingen/Project/Bioinformatical Tools}}
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{{GoettingenBlue}}
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== Computational Data ==
 +
=== Maps ===
 +
==== Tar_QC ====
 +
For Parts K777000 - K777008 the plasmid maps were constructed in ApE. Within the maps you will find annotated features, as well. To gain more information about the parts submitted by the iGEM team Göttingen 2012 [https://2012.igem.org/Team:Goettingen/iGEM/Parts click here]. <br>
 +
Moreover, the parts were completely sequenced (except for K777000) and aligned. The original data and the reviewed data are provided in the respective Zip- files. <br>
 +
* [https://static.igem.org/mediawiki/2012/f/fc/Tar_receptor_under_the_control_of_constitutive_promoter.zip ApE plasmid maps]
 +
*Sequencing results
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**[https://static.igem.org/mediawiki/2012/2/20/K777000_in_pSB1C3.zip K777000 in pSB1C3]
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**[https://static.igem.org/mediawiki/2012/e/e7/K777001_in_pSB1C3.zip K777001 in pSB1C3]
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**[https://static.igem.org/mediawiki/2012/9/90/K777002_in_pSB1C3.zip K777002 in pSB1C3]
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**[https://static.igem.org/mediawiki/2012/0/0a/K777003_in_pSB1C3.zip K777003 in pSB1C3]
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**[https://static.igem.org/mediawiki/2012/a/a8/K777004_in_pSB1C3.zip K777004 in pSB1C3]
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**[https://static.igem.org/mediawiki/2012/0/07/K777005_in_pSB1C3.zip K777005 in pSB1C3]
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**[https://static.igem.org/mediawiki/2012/6/61/K777006_in_pSB1C3.zip K777006 in pSB1C3]
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**[https://static.igem.org/mediawiki/2012/3/33/K777007_in_pSB1C3.zip K777007 in pSB1C3]
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**[https://static.igem.org/mediawiki/2012/5/52/K777008_in_pSB1C3.zip K777008 in pSB1C3]
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<body class="mediawiki ns-0 ltr page-Team_Goettingen">
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==== flhDC ====
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* [https://static.igem.org/mediawiki/2012/b/b6/K777100_in_pSB1C3.zip K777100 in pSB1C3 ApE plasmid map]
 +
==== fliC ====
 +
* [https://static.igem.org/mediawiki/2012/8/8b/K777109_in_pSB1C3.zip K777109 in pSB1C3 ApE plasmid map]
 +
==== motA ====
 +
* [https://static.igem.org/mediawiki/2012/3/37/K777113_in_pSB1C3.zip K777113 in pSB1C3 ApE plasmid map]
 +
==== motB ====
 +
* [https://static.igem.org/mediawiki/2012/0/09/K777117_in_pSB1C3.zip K777117 in pSB1C3 ApE plasmid map]
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                        <!-- start content -->
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==== yhjH ====
 +
* [https://static.igem.org/mediawiki/2012/3/3f/K777121_in_pSB1C3.zip K777121 in pSB1C3 ApE plasmid map]
 +
==== Constitutive promoter + RFP-constructs ====
 +
* [https://static.igem.org/mediawiki/2012/0/07/K777125-K777132.zip K777125-K777132 ApE plasmid maps]
 +
=== Primers ===
 +
* [https://static.igem.org/mediawiki/2012/4/43/Primer_Mutagenesis.zip Mutagenesis]
 +
* [https://static.igem.org/mediawiki/2012/f/fc/Primer_PCR.zip PCR]
 +
* [https://static.igem.org/mediawiki/2012/c/cf/Primer_QC.zip QuikChange]
 +
* [https://static.igem.org/mediawiki/2012/4/4b/Primer_Sequencing.zip Sequencing]
 +
* [https://static.igem.org/mediawiki/2012/4/45/Primer_Real-Time.zip Real-time]
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<style>
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=== Raw Datasets ===
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h1.firstHeading { display: none; }
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==== Characterization of constitutive promoters by qrtPCR ====
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p {text-align: justify;}
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<li>CP (crossing point) values and relative reinforcments of promoters from the [http://partsregistry.org/Promoters/Catalog/Anderson Anderson Family]:J23100, J23104, J23105, J23106, J23109, J23112, J23113, J23114 <br>The CP values ​​of the reference housekeeping genes (hkg) are reduced by the value of 3.32 for the dilution which have been used for the reference cDNA in the experiment.
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For detailed information of generation of data and data analyzes [https://2012.igem.org/Team:Goettingen/Project/Methods#Quantitative_Real-Time_PCR click here].
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a:link { color: #004080; text-decoration: none}
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{| class="wikitable"
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a:visited { color:##003090; text-decoration: none}
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|-
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a:hover { color:#f29400; text-decoration: none}
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! scope="col"| Promoter
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a:active { color:#f29400; text-decoration: none}
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! scope="col"|
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! scope="col"| CP1
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! scope="col"| CP2
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! scope="col"| CP3
 +
! scope="col"| Average
 +
! scope="col"| Standard variance
 +
|-
 +
! rowspan="3"| J23113 <br>(Calibrator)
 +
! J23113
 +
| align="right"| 23.7
 +
| align="right"| 24.46
 +
| align="right"| 24.51
 +
|-
 +
! J23113_hkg
 +
| align="right"| 5.48
 +
| align="right"| 5.33
 +
| align="right"| 4.57
 +
|- rowspan="2"
 +
! ΔCT Calibrator <br>(CP - CP_hkg)
 +
| align="right"| 18.22
 +
| align="right"| 18.93
 +
| align="right"| 19.94
 +
| align="right"| 19.03
 +
| align="right"| 0.71
 +
|-
 +
! rowspan="5"| J23106
 +
! J23106
 +
| align="right"| 23.25
 +
| align="right"| 22.37
 +
| align="right"| 22.44
 +
|-
 +
! J23106_hkg
 +
| align="right"| 4.66
 +
| align="right"| 5.58
 +
| align="right"| 5.59
 +
|-
 +
! ΔCT J23106
 +
| align="right"| 17.63
 +
| align="right"| 16.73
 +
| align="right"| 16.85
 +
|-
 +
! ΔΔCT J23106
 +
| align="right"| 1.4
 +
| align="right"| 2.3
 +
| align="right"| 2.18
 +
|-
 +
! Reinforcment
 +
| align="right"| 2.64
 +
| align="right"| 4.92
 +
| align="right"| 4.53
 +
| align="right"| 4.03
 +
| align="right"| 1.00
 +
|-
 +
! rowspan="5"| J23112
 +
! J23112
 +
| align="right"| 20.43
 +
| align="right"| 20.42
 +
| align="right"| 20.24
 +
|-
 +
! J23112_hkg
 +
| align="right"| 5.00
 +
| align="right"| 4.9
 +
| align="right"| 5.2
 +
|-
 +
! ΔCT J23112
 +
| align="right"| 15.43
 +
| align="right"| 15.52
 +
| align="right"| 15.04
 +
|-
 +
! ΔΔCT J23112
 +
| align="right"| 3.6
 +
| align="right"| 3.51
 +
| align="right"| 3.99
 +
|-
 +
! Reinforcment
 +
| align="right"| 12.13
 +
| align="right"| 11.39
 +
| align="right"| 15.89
 +
| align="right"| 13.14
 +
| align="right"| 1.97
 +
|-
 +
! rowspan="5"| J23114
 +
! J23112
 +
| align="right"| 20.35
 +
| align="right"| 20.07
 +
| align="right"| 20.88
 +
|-
 +
! J23114_hkg
 +
| align="right"| 5.77
 +
| align="right"| 6.13
 +
| align="right"| 5.75
 +
|-
 +
! ΔCT J23114
 +
| align="right"| 14.58
 +
| align="right"| 13.94
 +
| align="right"| 15.13
 +
|-
 +
! ΔΔCT J23114
 +
| align="right"| 4.45
 +
| align="right"| 5.09
 +
| align="right"| 3.90
 +
|-
 +
! Reinforcment
 +
| align="right"| 21.86
 +
| align="right"| 34.06
 +
| align="right"| 14.93
 +
| align="right"| 23.62
 +
| align="right"| 7.91
 +
|-
 +
! rowspan="5"| J23109
 +
! J23109
 +
| align="right"| 18.56
 +
| align="right"| 18.25
 +
| align="right"| 18.50
 +
|-
 +
! J23109_hkg
 +
| align="right"| 5.79
 +
| align="right"| 5.43
 +
| align="right"| 5.91
 +
|-
 +
! ΔCT J23109
 +
| align="right"| 12.77
 +
| align="right"| 12.82
 +
| align="right"| 12.59
 +
|-
 +
! ΔΔCT J23109
 +
| align="right"| 6.26
 +
| align="right"| 6.21
 +
| align="right"| 6.44
 +
|-
 +
! Reinforcment
 +
| align="right"| 76.64
 +
| align="right"| 74.03
 +
| align="right"| 86.82
 +
| align="right"| 79.16
 +
| align="right"| 5.52
 +
|-
 +
! rowspan="5"| J23105
 +
! J23105
 +
| align="right"| 16.05
 +
| align="right"| 16.21
 +
| align="right"| 16.13
 +
|-
 +
! J23105_hkg
 +
| align="right"| 4.98
 +
| align="right"| 5.22
 +
| align="right"| 5.18
 +
|-
 +
! ΔCT J23105
 +
| align="right"| 11.07
 +
| align="right"| 10.99
 +
| align="right"| 10.95
 +
|-
 +
! ΔΔCT J23105
 +
| align="right"| 7.96
 +
| align="right"| 8.04
 +
| align="right"| 8.08
 +
|-
 +
! Reinforcment
 +
| align="right"| 249.00
 +
| align="right"| 263.20
 +
| align="right"| 270.60
 +
| align="right"| 260.93
 +
| align="right"| 8.96
 +
|-
 +
! rowspan="5"| J23104
 +
! J23104
 +
| align="right"| 15.76
 +
| align="right"| 16.50
 +
| align="right"| 15.85
 +
|-
 +
! J23104_hkg
 +
| align="right"| 4.66
 +
| align="right"| 5.58
 +
| align="right"| 5.03
 +
|-
 +
! ΔCT J23104
 +
| align="right"| 11.10
 +
| align="right"| 10.92
 +
| align="right"| 10.82
 +
|-
 +
! ΔΔCT J23104
 +
| align="right"| 7.93
 +
| align="right"| 8.11
 +
| align="right"| 8.21
 +
|-
 +
! Reinforcment
 +
| align="right"| 243.88
 +
| align="right"| 276.28
 +
| align="right"| 296.11
 +
| align="right"| 272.09
 +
| align="right"| 21.53
 +
|-
 +
! rowspan="5"| J23100
 +
! J23100
 +
| align="right"| 14.02
 +
| align="right"| 13.53
 +
| align="right"| 14.21
 +
|-
 +
! J23100_hkg
 +
| align="right"| 4.06
 +
| align="right"| 4.23
 +
| align="right"| 5.12
 +
|-
 +
! ΔCT J23100
 +
| align="right"| 9.96
 +
| align="right"| 9.30
 +
| align="right"| 9.09
 +
|-
 +
! ΔΔCT J23100
 +
| align="right"| 9.07
 +
| align="right"| 9.73
 +
| align="right"| 9.94
 +
|-
 +
! Reinforcment
 +
| align="right"| 537.45
 +
| align="right"| 849.22
 +
| align="right"| 982.29
 +
| align="right"| 789.65
 +
| align="right"| 186.42
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Here you can find the according [https://static.igem.org/mediawiki/2012/4/4e/Qrt-PCR_18.0912_uploaded_igem_goettingen_2012.xls excel sheet] and a more detailed description of the [https://2012.igem.org/Team:Goettingen/Notebook/Results#.233_-_Chemoreceptor_Library results].<br>
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+
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+
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+
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+
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+
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+
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+
-
div.MenuBar#navi ul li:hover ul.DropDownMenu li:hover ul.SideMenu#MB1-DDM2-SM2,
+
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div.MenuBar#navi ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu#MB1-DDM2-SM2,
+
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/*
+
-
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+
-
Drop-Down Menu #2
+
-
Side Menu #3
+
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+
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div.MenuBar#navi ul li:hover ul.DropDownMenu li:hover ul.SideMenu#MB1-DDM2-SM3,
+
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+
-
  left: 15.5em  !important; /* Places the side menu to the right of the drop-down menu.
+
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+
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+
-
div.MenuBar#navi ul li:hover ul.DropDownMenu li:hover ul.SideMenu#MB1-DDM2-SM3,
+
-
div.MenuBar#navi ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu#MB1-DDM2-SM3,
+
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+
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</style>
+
-
 
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+
-
 
+
-
</p><div id="header"><img src="http://www.patrickreinke.de/igem/header.jpg" alt="Team Goettingen"></div>
+
-
<div class="MenuBar" id="navi">
+
-
        <ul>
+
-
                <li>
+
-
                        <a href="https://2012.igem.org/Team:Goettingen" style="color: white;">Home
+
-
                        <!--[if gt IE 6]><!--></a><!--<![endif]-->
+
-
                        <!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
+
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                        <!--[if lte IE 6]></td></tr></table></a><![endif]-->
+
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                </li>
+
-
                <li>
+
-
                        <a href="https://2012.igem.org/Team:Goettingen/Team" style="color: white;">Team<!--[if gt IE 6]><!--></a><!--<![endif]-->
+
-
                        <!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
+
-
                        <ul class="DropDownMenu" id="MB1-DDM6">
+
-
                        <li><a href="https://2012.igem.org/Team:Goettingen/Team"><span><span>Team members</span></span></a></li>
+
-
                        <li><a href="https://2012.igem.org/Team:Goettingen/Team#advisor"><span><span>Advisors</span></span></a></li>
+
-
                        <li><a href="https://2012.igem.org/Team:Goettingen/Team#alicia"><span><span>Students</span></span></a></li>
+
-
                        <li><a href="https://2012.igem.org/Team:Goettingen/Work_Impressions"><span><span>Work impressions</span></span></a></li>
+
-
                        </ul>
+
-
                        <!--[if lte IE 6]></td></tr></table></a><![endif]-->
+
-
                </li>
+
-
                <li>
+
-
                        <a href="https://2012.igem.org/Team:Goettingen/Project" style="color: white;">Project<!--[if gt IE 6]><!--></a><!--<![endif]-->
+
-
                        <!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
+
-
                        <ul class="DropDownMenu" id="MB1-DDM1">
+
-
                        <li><a href="https://2012.igem.org/Team:Goettingen/Project"><span><span>Our project</span></span></a></li>
+
-
                        <li><a href="https://2012.igem.org/Team:Goettingen/Material"><span><span>Material &amp; Methods</span></span></a>
+
-
                  </li><li><a href="https://2012.igem.org/Team:Goettingen/Chemotaxis"><span><span>Chemotaxis</span></span></a></li>
+
-
                        </ul>
+
-
                        <!--[if lte IE 6]></td></tr></table></a><![endif]-->
+
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                </li>
+
-
 
+
-
                <li>
+
-
                        <a href="https://2012.igem.org/Team:Goettingen/Notebook" style="color: white;">Notebook<!--[if gt IE 6]><!--></a><!--<![endif]-->
+
-
                        <!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
+
-
                                <ul class="DropDownMenu" id="MB1-DDM2">
+
-
                                <li><a href="https://2012.igem.org/Team:Goettingen/Notebook"><span><span>Notebook by month</span></span></a></li>
+
-
                                <li><a href="https://2012.igem.org/Team:Goettingen/Notebook#week"><span><span>Notebook by week</span></span></a></li>
+
-
                                </ul>
+
-
                                <!--[if lte IE 6]></td></tr></table></a><![endif]-->
+
-
                </li>
+
-
                <li>
+
-
                        <a href="https://2012.igem.org/Team:Goettingen/iGEM" style="color: white;">iGEM<!--[if gt IE 6]><!--></a><!--<![endif]-->
+
-
                        <!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
+
-
                                <ul class="DropDownMenu" id="MB1-DDM4">
+
-
                                <li><a href="https://2012.igem.org/Team:Goettingen/Saftey"><span><span>Saftey</span></span></a></li>
+
-
 
+
-
                                <li><a href="https://2012.igem.org/Team:Goettingen/Attributions"><span><span>Attributions</span></span></a></li>
+
-
                                </ul>
+
-
                                <!--[if lte IE 6]></td></tr></table></a><![endif]-->
+
-
                </li>
+
-
                <li>
+
-
                        <a href="https://2012.igem.org/Team:Goettingen/Modeling" style="color: white;">Modeling<!--[if gt IE 6]><!--></a><!--<![endif]-->
+
-
                        <!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
+
-
                                <ul class="DropDownMenu" id="MB1-DDM5">
+
-
                                <li><a href="https://2012.igem.org/Team:Goettingen/Modeling"><span><span>Modeling</span></span></a></li>
+
-
                                <li><a href="https://2012.igem.org/Team:Goettingen/Parts"><span><span>Parts Submitted</span></span></a></li>
+
-
                        <!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
+
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                                        <!--[if lte IE 6]></td></tr></table></a><![endif]-->
+
-
                                </li>
+
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+
-
                                </ul>
+
-
                                <!--[if lte IE 6]></td></tr></table></a><![endif]-->
+
-
                </li>
+
-
                <li style="width: 160px">
+
-
                        <a href="https://2012.igem.org/Team:Goettingen/Human_Practice/Human_practice" style="color: white;">Human Practice<!--[if gt IE 6]><!--></a><!--<![endif]-->
+
-
                        <!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
+
-
                                <ul class="DropDownMenu" id="MB1-DDM2-SM3">
+
-
                              <li><a href="https://2012.igem.org/Team:Goettingen/Human_Practice/Human_practice"><span><span>Human Practice</span></span></a></li>
+
-
                              <li><a href="https://2012.igem.org/Team:Goettingen/Human_Practice/Flash_coli"><span><span>Flash Coli</span></span></a></li>
+
-
 
+
-
 
+
-
                                </ul>
+
-
                                <!--[if lte IE 6]></td></tr></table></a><![endif]-->
+
-
                </li>
+
-
 
+
-
                <li>
+
-
                        <a href="https://2012.igem.org/Team:Goettingen/Sponsors" style="color: white;">Sponsors</a>
+
-
                </li>
+
-
        </ul>
+
-
 
+
-
</div>
+
-
 
+
-
 
+
-
<p></p>
+
-
<table>
+
-
                                <!-- Text body -->
+
-
<tbody>
+
-
 
+
-
<tr valign="top" align="left">
+
-
<td style="padding: 0pt 20px 0pt 0pt;" width="910px">
+
-
<font face="Verdana" size="-1">
+
-
 
+
-
                                <!-- Ab hier kannst du editieren -->
+
-
 
+
-
<h2><b>Overview of Bioinformatical Tools</b></h2>
+
-
<p align="justify" style="line-height:1.6em">
+
-
<h2 style="margin:3px; background:#cedff2; font-size:120%; font-weight:bold; border:1px solid #a3b0bf; text-align:left; color:#000; padding:0.2em 0.4em;">Bioinformatical Tools</h2>
+
-
<ul>
+
-
<li> <a href="http://biologylabs.utah.edu/jorgensen/wayned/ape/">A plasmid Editor ApE </a> - Use of ApE </li>
+
-
<li> <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi">Alignment of Sequences </a> - BLAST: Basic Local Alignment Search Tool of NCBI </li>
+
-
<li> <a href="http://www.iit-biotech.de/iit-cgi/oligo-tm.pl"> T<sub>m</sub> calculator </a> - Calculator for Primer Melting Temperature </li>
+
-
<li> <a href="http://www.fermentas.com/en/tools/doubledigest/">Double Digest Finder </a> - Double Digest Finder of Thermo Scientific </li>
+
-
<li> <a href="http://www.neb.com/nebecomm/EnzymeFinderSearchbySequence.asp">Enzyme Finder </a> - Enzyme Finder of NEB </li>
+
-
<li> <a href="http://tools.neb.com/NEBcutter2/">NEBcutter V2.0 </a> - NEBcutter V2.0 </li>
+
-
<li> <a href="http://www.ncbi.nlm.nih.gov/gorf/gorf.html"> ORF Finder </a> - ORF Finder of NCBI </li>
+
-
<li> <a href="http://rebase.neb.com/rebase/rebase.html">RE Base </a> - The Restriction Enzyme Database RE Base of NEB </li>
+
-
</ul>
+
-
<br>
+
-
<br>
+
-
<br>
+
-
<br>
+
-
<br>
+
-
<tbody><tr valign="top" align="left">
+
-
 
+
-
<td style="padding: 0pt 20px 0pt 0pt;" width="650px">
+
-
<font face="Verdana" size="-1">
+
-
<h2><b>A plasmid Editor ApE</b></h2>
+
-
 
+
-
<p align="justify" style="line-height:1.6em">
+
-
The plasmid Editor ApE by M. Wayne Davis is a free ware program conceived for both Windows (XP, Vista and 7) and Mac (OS X v10.5 and above). It can be downloaded from <a href="http://biologylabs.utah.edu/jorgensen/wayned/ape/">http://biologylabs.utah.edu/jorgensen/wayned/ape/], [06/29/2012]</a>. The program offers lots of applications required for cloning processes, e.g. construction of plasmid maps, primer design, sequence alignments, management of sequences, ORF finder, Tm calculator, translation of nucleotide sequences and a lot more. ApE is compatible for the handling of common sequencing formatted .seq and .ab1 files. For further information visit the ApE homepage. Moreover, the hoster´s of the program take care about an <a href="http://ape-a-plasmid-editor.wikispaces.com/">ApE Wiki, [08/01/2012]</a> where you can find help and advice if questions in the use of ApE pop up.<br>
+
-
<br>
+
-
</p>
+
-
 
+
-
<h3><b>Primer Design with ApE</b></h3>
+
-
<p align="justify" style="line-height:1.6em">
+
-
Primers depend mainly on the chosen criteria. Yet, the specifity and the tendency to form hair-pins drastically reduces straight forward PCR amplification of genes.
+
-
ApE also offers a primer design feature. <br>
+
-
<ol>
+
-
<blockquote>
+
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<li> Highlight the sequence to which the primer should bind. Recognize that given standard minimum and maximum length is 20 bp and 25 bp, respectively. Nevertheless, these options can be altered. </li>
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<li> Select "Tools -> Find Primers". A new window Find primers will emerge offering lots of different manipulatable attributes. </li>
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<li> Click "OK" to see the possible primers. </li>
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</blockquote>
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</ol>
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</p>
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<h3><b>Primer Binding with ApE</b></h3>
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<p align="justify" style="line-height:1.6em">
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[[File:ApE Primer01.jpg|thumb|250px|'''Fig. 1: ApE window for binding of primers''']]
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In this example, ApE is used to find the binding site on Lambda DNA for primer with a specific sequence.  <br>
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<ol>
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<blockquote>
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<li> Open ApE and paste the desired sequence, for which the primer is designated, in the sequence field (or open according .ape file, if made before. </li>
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<li> Go to Edit>Find (or use Ctrl+F). </li>
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<li> Paste the primer sequence and check "also find rev-com of string" (the primer may be identical to (a part of) the opposite DNA strand.) and click the "Find Next" button, as shown in Fig. 1.  </li>
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<li> The in blue highlighted sequence appears to be the desired primer sequence annealing to the template sequence. Check also if primer is indeed the reverse complement. Below the icon bar, one can find information about the length of the primer 30 nucleotides and the binding site. </li>
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For an illustrative description of each steps, please follow <a href="http://www.bioinformatics.nl/molbi/SCLResources/Bioinformatics.htm#Finding_primer_binding_sites_using_ApE">http://www.bioinformatics.nl/molbi/SCLResources/Bioinformatics.htm#Finding_primer_binding_sites_using_ApE; [06/29/2012] </a>. </li>
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</blockquote>
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</ol>
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</p>
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<h3><b>Find restriction sites and fragment lenghts with ApE</b></h3>
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<p align="justify" style="line-height:1.6em">
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<ol>
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<blockquote>
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<li> Start ApE and open desired sequence. </li>
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<li> Go to the Enzyme Selector (or use Ctrl+E) and click on the wanted restriction enzymes; the amount of restriction sites will be indicated in brackets.</li>
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<li> One can now continue with different options:
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</blockquote>
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<blockquote>
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<ul>
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<li> searching different restriction enzymes with particular properties applying the various buttons in the "Select panel",</li>
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<li> or highlighting the restiction site within the given sequence by pressing "Highlight" button, </li>
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<li> or simulating a restriction <i>in silico</i> by klicking on the "Digest" button.</li>
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</ul>
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</blockquote>
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<p align="justify" style="line-height:1.6em">
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A new window will appear showing the digestion results. Additional information about the different bands can be received by hovering the mouse arrow over the bands, map or text. A convenient way to see the respective sequence behind a digested fragment is by simply klicking on the fragment within the digest window.
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For a description with the use of pictures for each step, please follow <a href="http://www.bioinformatics.nl/molbi/SCLResources/ApE_and_lambda.htm">http://www.bioinformatics.nl/molbi/SCLResources/ApE_and_lambda.htm; [06/29/2012]</a>.
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</p>
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<h3><b>Blasting Sequences</b></h3>
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<p align="justify" style="line-height:1.6em">
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For blasting two Sequences:
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<ol>
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<li> Open two sequences on ApE. </li>
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<li> Select "Tools -> Align Two Sequences".
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</ol>
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<br>
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For blasting multiple Sequences:
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<ol>
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<li> Open multiple sequences on ApE. </li>
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<li> Select "Tools -> Align Sequences". </li>
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</ol>
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</p>
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<p align="justify" style="line-height:1.6em">
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It is important to note that the opening chronology of the ApE files will matter in the order of the alignment sequences. Those will show up in according sequence from top to bottom.
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Mismatches will be highlighted in red color, whereas matches will use the respective nucleotide linked with a dash. By double-clicking on any base pair within the sequence alignment, the sequence corresponding to this location will appear in the sequence ApE window.
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</p>
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<h3><b>Finding the ORF</b></h3>
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<p align="justify" style="line-height:1.6em">
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<ol>
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<li> Under "ORFs -> Find Next (or Ctrl+>) / Find Previous (or Ctrl+<)" open reading frames, i. e sequences beginning with a start codon ATG and end with one of the stop codons, become visible.  </li>
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<li> These ORFs can be translated using "ORFs -> Selection Translate" for direct amino acid sequence in the current displayed selection or by creating a new window "ORFs (or Ctrl+T)-> Translate" listing the aa sequence and enabling to link the amino acids with the nucleotides, respectively. The translated sequence can be chosen in 1- or 3-letter code. </li>
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</ol>
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</p>
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<h3><b>General Remarks </b></h3>
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<p align="justify" style="line-height:1.6em">
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<ul>
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<li> While copying features from one file to another, it is obligatory to have the file containing those features still open.  </li>
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<li> Addition of extra enzymes is possible only via the "Enzyme Editor (or Ctrl+E) -> Enzymes -> New Enzyme". To save these changes in the program folders ApE, use "Enzyme Editor (or Ctrl+E) -> File -> Save Current Enzymes as Default". For permanent saving exceeding new installing of the program, copy your Default file within the ApE program pathway. After installing paste this file in the corresponding folder. </li>
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Features in the DNA sequences can be labeled, selecting "Features (or Ctrl+.) -> New Feature" allowing to mark the standard BioBrick restriction sites obvious or e.g. antibiotic resistances. These annotations are also saved. Moreover, it has a preexisting Feature Library which can be used for easily see important regions. </li>
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</ul>
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Latest revision as of 23:49, 26 September 2012

Deutsch  / English 

Contents

Computational Data

Maps

Tar_QC

For Parts K777000 - K777008 the plasmid maps were constructed in ApE. Within the maps you will find annotated features, as well. To gain more information about the parts submitted by the iGEM team Göttingen 2012 click here.
Moreover, the parts were completely sequenced (except for K777000) and aligned. The original data and the reviewed data are provided in the respective Zip- files.

flhDC

fliC

motA

motB

yhjH

Constitutive promoter + RFP-constructs

Primers

Raw Datasets

Characterization of constitutive promoters by qrtPCR

  • CP (crossing point) values and relative reinforcments of promoters from the [http://partsregistry.org/Promoters/Catalog/Anderson Anderson Family]:J23100, J23104, J23105, J23106, J23109, J23112, J23113, J23114
    The CP values ​​of the reference housekeeping genes (hkg) are reduced by the value of 3.32 for the dilution which have been used for the reference cDNA in the experiment. For detailed information of generation of data and data analyzes click here.
    Promoter CP1 CP2 CP3 Average Standard variance
    J23113
    (Calibrator)     		J23113 23.7 24.46 24.51
    J23113_hkg 5.48 5.33 4.57
    ΔCT Calibrator
    (CP - CP_hkg)     		18.22 18.93 19.94 19.03 0.71
    J23106 J23106 23.25 22.37 22.44
    J23106_hkg 4.66 5.58 5.59
    ΔCT J23106 17.63 16.73 16.85
    ΔΔCT J23106 1.4 2.3 2.18
    Reinforcment 2.64 4.92 4.53 4.03 1.00
    J23112 J23112 20.43 20.42 20.24
    J23112_hkg 5.00 4.9 5.2
    ΔCT J23112 15.43 15.52 15.04
    ΔΔCT J23112 3.6 3.51 3.99
    Reinforcment 12.13 11.39 15.89 13.14 1.97
    J23114 J23112 20.35 20.07 20.88
    J23114_hkg 5.77 6.13 5.75
    ΔCT J23114 14.58 13.94 15.13
    ΔΔCT J23114 4.45 5.09 3.90
    Reinforcment 21.86 34.06 14.93 23.62 7.91
    J23109 J23109 18.56 18.25 18.50
    J23109_hkg 5.79 5.43 5.91
    ΔCT J23109 12.77 12.82 12.59
    ΔΔCT J23109 6.26 6.21 6.44
    Reinforcment 76.64 74.03 86.82 79.16 5.52
    J23105 J23105 16.05 16.21 16.13
    J23105_hkg 4.98 5.22 5.18
    ΔCT J23105 11.07 10.99 10.95
    ΔΔCT J23105 7.96 8.04 8.08
    Reinforcment 249.00 263.20 270.60 260.93 8.96
    J23104 J23104 15.76 16.50 15.85
    J23104_hkg 4.66 5.58 5.03
    ΔCT J23104 11.10 10.92 10.82
    ΔΔCT J23104 7.93 8.11 8.21
    Reinforcment 243.88 276.28 296.11 272.09 21.53
    J23100 J23100 14.02 13.53 14.21
    J23100_hkg 4.06 4.23 5.12
    ΔCT J23100 9.96 9.30 9.09
    ΔΔCT J23100 9.07 9.73 9.94
    Reinforcment 537.45 849.22 982.29 789.65 186.42

    Here you can find the according excel sheet and a more detailed description of the results.


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    Retrieved from "http://2012.igem.org/Team:Goettingen/Project/Bioinformatical_Tools"