Team:Goettingen/Project/Bioinformatical Tools

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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 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.

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.

↑ Back to top!

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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
+**[https://static.igem.org/mediawiki/2012/2/20/K777000_in_pSB1C3.zip K777000 in pSB1C3]
+**[https://static.igem.org/mediawiki/2012/e/e7/K777001_in_pSB1C3.zip K777001 in pSB1C3]
+**[https://static.igem.org/mediawiki/2012/9/90/K777002_in_pSB1C3.zip K777002 in pSB1C3]
+**[https://static.igem.org/mediawiki/2012/0/0a/K777003_in_pSB1C3.zip K777003 in pSB1C3]
+**[https://static.igem.org/mediawiki/2012/a/a8/K777004_in_pSB1C3.zip K777004 in pSB1C3]
+**[https://static.igem.org/mediawiki/2012/0/07/K777005_in_pSB1C3.zip K777005 in pSB1C3]
+**[https://static.igem.org/mediawiki/2012/6/61/K777006_in_pSB1C3.zip K777006 in pSB1C3]
+**[https://static.igem.org/mediawiki/2012/3/33/K777007_in_pSB1C3.zip K777007 in pSB1C3]
+**[https://static.igem.org/mediawiki/2012/5/52/K777008_in_pSB1C3.zip K777008 in pSB1C3]
-<body class="mediawiki ns-0 ltr page-Team_Goettingen">
+==== flhDC ====
+* [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]
-                        <!-- start content -->
+==== 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]
-<style>
+=== Raw Datasets ===
-h1.firstHeading { display: none; }
+==== Characterization of constitutive promoters by qrtPCR ====
-p {text-align: justify;}
+<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.
+For detailed information of generation of data and data analyzes [https://2012.igem.org/Team:Goettingen/Project/Methods#Quantitative_Real-Time_PCR click here].
-a:link { color: #004080; text-decoration: none}
+{| class="wikitable"
-a:visited { color:##003090; text-decoration: none}
+|-
-a:hover { color:#f29400; text-decoration: none}
+! scope="col"| Promoter
-a:active { color:#f29400; text-decoration: none}
+! scope="col"|
+! scope="col"| CP1
+! scope="col"| CP2
+! 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
-#bodyContent { padding: 10px auto; width: 910px; margin: auto; clear: none; }
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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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-</p><div id="header"><img src="http://www.patrickreinke.de/igem/header.jpg" alt="Team Goettingen"></div>
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-</div>
-<p></p>
-<table>
-                                 <!-- Text body -->
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-<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">
-Here, an useful list of computational and bioinformatical tools is provided. All of these programs are regularly used by the students to do the cloning process. <br>
-<br>
-<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="#ApE">A plasmid Editor ApE </a> - Use of ApE </li>
-<li> <a href="#Blast">Alignment of Sequences </a> - BLAST: Basic Local Alignment Search Tool of NCBI </li>
-<li> <a href="#Tm calc"> T<sub>m</sub> calculator </a> - Calculator for Primer Melting Temperature </li>
-<li> <a href="#DD Finder"> Double Digest Finder </a> - Double Digest Finder of Thermo Scientific </li>
-<li> <a href="#Enzyme Finder">Enzyme Finder </a> - Enzyme Finder of NEB </li>
-<li> <a href="#NEBcutter">NEBcutter V2.0 </a> - NEBcutter V2.0 </li>
-<li> <a href="#ORF Finder"> ORF Finder </a> - ORF Finder of NCBI </li>
-<li> <a href="#RE Base">RE Base </a> - The Restriction Enzyme Database RE Base of NEB </li>
-</ul>
-<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 name="Ape"><a href="http://biologylabs.utah.edu/jorgensen/wayned/ape/">A plasmid Editor ApE</a></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>
-<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>
-<li> Select "Tools -> Find Primers". A new window Find primers will emerge offering lots of different manipulatable attributes. </li>
-<li> Click "OK" to see the possible primers. </li>
-</blockquote>
-</ol>
-</p>
-<h3><b>Primer Binding with ApE</b></h3>
-<p align="justify" style="line-height:1.6em">
-ApE also aids to create specific primer on a desired DNA.  <br>
-<ol>
-<blockquote>
-<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>
-<li> Go to "Edit>Find" (or use Ctrl+F). </li>
-<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>
-<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>
-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>
-</blockquote>
-</ol>
-</p>
-<h3><b>Find restriction sites and fragment lenghts with ApE</b></h3>
-<p align="justify" style="line-height:1.6em">
-<ol>
-<blockquote>
-<li> Start ApE and open desired sequence. </li>
-<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>
-<li> One can now continue with different options:
-</blockquote>
-<blockquote>
-<ul>
-<li> searching different restriction enzymes with particular properties applying the various buttons in the "Select panel",</li>
-<li> or highlighting the restiction site within the given sequence by pressing "Highlight" button, </li>
-<li> or simulating a restriction <i>in silico</i> by klicking on the "Digest" button.</li>
-</ul>
-</blockquote>
-</ol>
-</p>
-<p align="justify" style="line-height:1.6em">
-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.
-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>.
-</p>
-<h3><b>Blasting Sequences</b></h3>
-<p align="justify" style="line-height:1.6em">
-For blasting two Sequences:
-<ol>
-<li> Open two sequences on ApE. </li>
-<li> Select "Tools -> Align Two Sequences".
-</ol>
-<br>
-For blasting multiple Sequences:
-<ol>
-<li> Open multiple sequences on ApE. </li>
-<li> Select "Tools -> Align Sequences". </li>
-</ol>
-</p>
-<p align="justify" style="line-height:1.6em">
-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.
-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.
-</p>
-<h3><b>Finding the ORF</b></h3>
-<p align="justify" style="line-height:1.6em">
-<ol>
-<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>
-<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>
-</ol>
-</p>
-<h3><b>General Remarks </b></h3>
-<p align="justify" style="line-height:1.6em">
-<ul>
-<li> While copying features from one file to another, it is obligatory to have the file containing those features still open.   </li>
-<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>
-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>
-</ul>
-</p>
-</p>
-<br>
-<br>
-<br>
-<h2><b><a name="Blast"><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi">Alignment of Sequences</a></b></h2>
-<p align="justify" style="line-height:1.6em">
-This <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi">link</a> allows the alignment of two or even multiple given sequences.
-To become more informed how to do the sequence alignment with BLAST follow <a href="http://www.bioinformatics.nl/molbi/SCLResources/Bioinformatics.htm#Alignment_of_two_given_sequences_">http://www.bioinformatics.nl/molbi/SCLResources/Bioinformatics.htm#Alignment_of_two_given_sequences_; [06/29/2012]</a>.
-<br>
-<br>
-</p>
-<h2><b><a name="Tm calc"><a href="http://www.iit-biotech.de/iit-cgi/oligo-tm.pl"> T<sub>m</sub> calculator </a></b></h2>
-<p align="justify" style="line-height:1.6em">
-This <a href="http://www.iit-biotech.de/iit-cgi/oligo-tm.pl">link</a> provides an on-line calculation form for the melting temperature Tm of PCR primers referring to the so-called Nearest Neighbour method.
-<br>
-<br>
-</p>
-<h2><b><a name="DD finder"><a href="http://www.fermentas.com/en/tools/doubledigest/">Double Digest Finder </a></b></h2>
-<p align="justify" style="line-height:1.6em">
-This <a href="http://www.fermentas.com/en/tools/doubledigest/">link</a> helps to find the appropriate reaction conditions while cleaving a DNA substrate with two restriction enzymes simultaneously as double digestion is a common timesaving procedure. The Thermo Scientific Double Digest Finder tool is applied by selecting the two restriction enzymes and submitting the query. It gives the reaction conditions amenable to any two Thermo Scientific restriction enzymes.
-<br>
-<br>
-</p>
-<h2><b><a name="Enzyme Finder"><a href="http://www.neb.com/nebecomm/EnzymeFinderSearchbySequence.asp">Enzyme Finder </a></b></h2>
-<p align="justify" style="line-height:1.6em">
-This <a href="http://www.neb.com/nebecomm/EnzymeFinderSearchbySequence.asp">link</a> leads to a tool which allows for selection of restriction enzymes by name, sequence, overhang, or type. It should be noted that the single letter code nomenclature should be entered for restriction sites. The search results appear in a list having enzymes supplied by NEB at the top with corresponding displayed links.
-<br>
-<br>
-</p>
-<h2><b><a name="NEBcutter"><a href="http://tools.neb.com/NEBcutter2/">NEBcutter V2.0 </a></b></h2>
-<p align="justify" style="line-height:1.6em">
-This <a href="http://tools.neb.com/NEBcutter2/">link</a> will lead one to the NEBcutter: a program to cleave DNA with restriction enzymes.
-By submitting a maximum size of the input file of 1 MByte or a maximum sequence length of 300 kb, a linearized sequence restriction map will
-be the result containing the marked restriction enzyme sites. The map also indicates the fashion of the sticky or blunted end cutters.
-Moreover, additional effects like methylation of the DNA sequence are given, too.
-<br>
-<br>
-</p>
-<h2><b><a name="ORF Finder"><a href="http://www.ncbi.nlm.nih.gov/projects/gorf/"> ORF Finder </a></b></h2>
-<p align="justify" style="line-height:1.6em">
-"The ORF Finder (Open Reading Frame Finder) is a graphical analysis tool which finds all open reading frames of a selectable minimum size in an
-user's sequence or in a sequence already in the database.
-This tool identifies all open reading frames using the standard or alternative genetic codes. The deduced amino acid sequence can be saved in
-various formats and searched against the sequence database using the WWW BLAST server. The ORF Finder should be helpful in preparing complete
-and accurate sequence submissions. It is also packaged with the Sequin sequence submission software" (<a href="http://www.ncbi.nlm.nih.gov/projects/gorf/">http://www.ncbi.nlm.nih.gov/projects/gorf/; [06/29/2012]</a>).
-This <a href="http://www.ncbi.nlm.nih.gov/projects/gorf/">link</a> aids to find all open reading frames (ORFs) in a given sequence. It is an ideal alternative to the ApE ORF finding feature if an ApE sequence file has not been constructed yet or if ApE is not installed at the used computer.
-<br>
-<br>
-</p>
-<h2><b><a name="RE Base"><a href="http://rebase.neb.com/rebase/rebase.html">RE Base </a></b></h2>
-<p align="justify" style="line-height:1.6em">
-This <a href="http://rebase.neb.com/rebase/rebase.html">link</a> encompasses comprehensive information about restriction enzymes and is the official RE Database by NEB.
-It provides for instance information of suppliers, recognition sequence, isoschizomers and the restriction enzyme type. In regard of a single enzyme also the organism and organism type with respective growth temperature behind the abbreviation is listed.
-Choose the search enzyme names or the recognition sequence search catagory, and type a keyword (e.g. ecor or gaattc) to quickly find info about specific enzymes and click REbase list to find more specialised information.
-In this example, <i>BamH</i>I was searched within the RE Base:
-<ul>
-<li>Acronym: <i>BamH</i> </li>
-<li>Prototype: <i>BamH</i>I</li>
-<li>Org #: 208 </li>
-<li><i>Organism: Bacillus amyloliquefaciens H</i></li>
-<li>Organism type: bacteria</li>
-<li>Organism source: ATCC 49763   (ATCC LINK)</li>
-<li>Growth Temperature: 37°C</li>
-<li>Experimental Evidence: biochemistry </li>
-<li>Exhibits star activity </li>
-<li>Enzyme gene cloned. </li>
-<li>Enzyme gene sequenced.</li>
-<li>Crystal data present.</li>
-<li>Kinetics data present.</li>
-<li>Molecular Weight: 24569</li>
-</ul>
-Have also a look at <a href="http://www.neb.com/nebecomm/EnzymeFinderSearchbySequence.asp"> Enzyme Finder</a> as alternative source of information.
-<br>
-</p>
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Team:Goettingen/Project/Bioinformatical Tools

From 2012.igem.org

Latest revision as of 23:49, 26 September 2012

Contents

Computational Data

Maps

Tar_QC

flhDC

fliC

motA

motB

yhjH

Constitutive promoter + RFP-constructs

Primers

Raw Datasets

Characterization of constitutive promoters by qrtPCR