Team:SUSTC-Shenzhen-B/introduction

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<title>SUSTC iGEM Theme - Free CSS Template</title>
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<meta name="keywords" content="beauty class, free theme, website design, bokehs, pink, orange, templatemo, CSS, HTML" />
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<meta name="author" content="tengattack" />
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<meta name="description" content="Beauty Class Theme, pinky background gradient with bokehs, free CSS template provided by templatemo.com" />
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                <h2>Introduction</h2>
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                <h3>Transcription：</h3>
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<p>The transcription stage, the reading of genetic information from DNA, is composed of promoter binding and the activation of RNA polymerase, RNA transcript initiation and promoter escape, RNA transcript elongation, and transcript termination, and release. </p>
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<p>We use three main algorithms of calculating which were put forward by different papers. They are all based on calculating the score or Gibbs free energy of the stem-loop and T-tail, and then we use some of our own experiment data of those typical terminators to get the fitting function of terminator efficiency with the score and ΔG. We also use other experment data to prove and correct our function to make it better.</p>
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<p>The function of the software is brief that users only need to input the sequency of their terminator and then it can output the structure and efficiency of the terminator. For those users who can connect to the internet, we have our website www.terminatorefficiency.com for them to use without download our software, and for those who cannot, they can download our software to use.</p>
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                <h3>Tools</h3>
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                <p>Because we are a software producer, we need to use different tools to write our software. First, our algorithm were written using c# in vs2010, in order to get the aim that the software can run in the back of the user interface. Second, the software user interface was wrote in vs2010 using WPF directly which we thought is the easiest and most beautiful technology for windows software. The first and second version of the website was made by three software: Photoshop, which was used for getting great picture, Dreamwaver, which was used for making the structure of the interface, and vs2010, which was used for connecting the UI with our algorithm. When everything was done, we applied our own realm name and server to achieve the dream of building the website. Although the processes of debugging and building the server were very hard, we make our software successfully.</p>
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                <h3>Brief Flow Chart</h3>
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            <div class="col col13 no_margin_right">
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                <h2>Online Tool</h2>
+
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                <p>This is the address of our “transcriptional terminator efficiency calculator” website.  </p>
+
-
                <ul class="tmo_ul_list">
+
-
                    <li><a href="http://www.terminatorefficiency.com/">TTEC</a></li>
+
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                    <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/Tutorial">Tutorial</a></li>
+
-
                </ul>
+
-
                <br>
+
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                <h3>acknowledgements</h3>
+
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                <p>This is the first time that we join this competition, we got many help from some companies and other teams. thanks for their help and supports!</p>
+
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                <ul class="tmo_ul_list">
+
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                    <li><a href="http://www.sustc.edu.cn/">SUSTC</a></li>
+
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                    <li><a href="http://www.genomics.cn/index">BGI</a></li>
+
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                    <li><a href="http://www.siat.ac.cn/">SIAT</a></li>
+
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                </ul>
+
 +
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.pp_content_container .pp_right{background:url(../images/facebook/contentPatternRight.png) top right repeat-y}div.facebook .pp_expand{background:url(../images/facebook/sprite.png) -31px -26px no-repeat;cursor:pointer}div.facebook .pp_expand:hover{background:url(../images/facebook/sprite.png) -31px -47px no-repeat;cursor:pointer}div.facebook .pp_contract{background:url(../images/facebook/sprite.png) 0 -26px no-repeat;cursor:pointer}div.facebook .pp_contract:hover{background:url(../images/facebook/sprite.png) 0 -47px no-repeat;cursor:pointer}div.facebook .pp_close{background:url(../images/facebook/sprite.png) -1px -1px no-repeat;cursor:pointer;height:22px;width:22px}div.facebook .pp_description{margin:0 37px 0 0}div.facebook .pp_loaderIcon{background:url(../images/facebook/loader.gif) center center no-repeat}div.facebook .pp_arrow_previous{background:url(../images/facebook/sprite.png) 0 -71px no-repeat;height:22px;margin-top:0;width:22px}div.facebook .pp_arrow_previous.disabled{background-position:0 -96px;cursor:default}div.facebook .pp_arrow_next{background:url(../images/facebook/sprite.png) -32px -71px no-repeat;height:22px;margin-top:0;width:22px}div.facebook .pp_arrow_next.disabled{background-position:-32px -96px;cursor:default}div.facebook .pp_nav{margin-top:0}div.facebook .pp_nav p{font-size:15px;padding:0 3px 0 4px}div.facebook .pp_nav .pp_play{background:url(../images/facebook/sprite.png) -1px -123px no-repeat;height:22px;width:22px}div.facebook .pp_nav .pp_pause{background:url(../images/facebook/sprite.png) -32px -123px no-repeat;height:22px;width:22px}div.facebook .pp_next:hover{background:url(../images/facebook/btnNext.png) center right no-repeat;cursor:pointer}div.facebook .pp_previous:hover{background:url(../images/facebook/btnPrevious.png) center left no-repeat;cursor:pointer}div.facebook .pp_bottom .pp_left{background:url(../images/facebook/sprite.png) -88px -80px no-repeat}div.facebook .pp_bottom .pp_middle{background:url(../images/facebook/contentPatternBottom.png) top left repeat-x}div.facebook .pp_bottom .pp_right{background:url(../images/facebook/sprite.png) -110px -80px no-repeat}div.pp_pic_holder a:focus{outline:0}div.pp_overlay{background:#000;display:none;left:0;position:absolute;top:0;width:100%;z-index:9500}div.pp_pic_holder{display:none;position:absolute;width:100px;z-index:10000}.pp_content{height:40px;min-width:40px}* html .pp_content{width:40px}.pp_content_container{position:relative;text-align:left;width:100%}.pp_content_container .pp_left{padding-left:20px}.pp_content_container .pp_right{padding-right:20px}.pp_content_container .pp_details{float:left;margin:10px 0 2px}.pp_description{display:none;margin:0}.pp_social{float:left;margin:0}.pp_social .facebook{float:left;margin-left:5px;overflow:hidden;width:55px}.pp_social .twitter{float:left}.pp_nav{clear:right;float:left;margin:3px 10px 0 0}.pp_nav p{float:left;margin:2px 4px;white-space:nowrap}.pp_nav .pp_play,.pp_nav .pp_pause{float:left;margin-right:4px;text-indent:-10000px}a.pp_arrow_previous,a.pp_arrow_next{display:block;float:left;height:15px;margin-top:3px;overflow:hidden;text-indent:-10000px;width:14px}.pp_hoverContainer{position:absolute;top:0;width:100%;z-index:2000}.pp_gallery{display:none;left:50%;margin-top:-50px;position:absolute;z-index:10000}.pp_gallery div{float:left;overflow:hidden;position:relative}.pp_gallery ul{float:left;height:35px;margin:0 0 0 5px;padding:0;position:relative;white-space:nowrap}.pp_gallery ul a{border:1px rgba(0,0,0,.5) solid;display:block;float:left;height:33px;overflow:hidden}.pp_gallery ul a img{border:0}.pp_gallery li{display:block;float:left;margin:0 5px 0 0;padding:0}.pp_gallery li.default a{background:url(../images/facebook/default_thumbnail.gif) 0 0 no-repeat;display:block;height:33px;width:50px}.pp_gallery .pp_arrow_previous,.pp_gallery .pp_arrow_next{margin-top:7px!important}a.pp_next{background:url(../images/light_rounded/btnNext.png) 10000px 10000px no-repeat;display:block;float:right;height:100%;text-indent:-10000px;width:49%}a.pp_previous{background:url(../images/light_rounded/btnNext.png) 10000px 10000px no-repeat;display:block;float:left;height:100%;text-indent:-10000px;width:49%}a.pp_expand,a.pp_contract{cursor:pointer;display:none;height:20px;position:absolute;right:30px;text-indent:-10000px;top:10px;width:20px;z-index:20000}a.pp_close{display:block;line-height:22px;position:absolute;right:0;text-indent:-10000px;top:0}.pp_loaderIcon{display:block;height:24px;left:50%;margin:-12px 0 0 -12px;position:absolute;top:50%;width:24px}#pp_full_res{line-height:1!important}#pp_full_res .pp_inline{text-align:left}#pp_full_res .pp_inline p{margin:0 0 15px}div.ppt{color:#fff;display:none;font-size:17px;margin:0 0 5px 15px;z-index:9999}div.pp_default .pp_content,div.light_rounded .pp_content{background-color:#fff}div.pp_default #pp_full_res .pp_inline,div.light_rounded .pp_content .ppt,div.light_rounded #pp_full_res .pp_inline,div.light_square .pp_content .ppt,div.light_square #pp_full_res .pp_inline,div.facebook .pp_content .ppt,div.facebook #pp_full_res .pp_inline{color:#000}div.pp_default .pp_gallery ul li a:hover,div.pp_default .pp_gallery ul li.selected a,.pp_gallery ul a:hover,.pp_gallery li.selected a{border-color:#fff}div.pp_default .pp_details,div.light_rounded .pp_details,div.dark_rounded .pp_details,div.dark_square .pp_details,div.light_square .pp_details,div.facebook .pp_details{position:relative}div.light_rounded .pp_top .pp_middle,div.light_rounded .pp_content_container .pp_left,div.light_rounded .pp_content_container .pp_right,div.light_rounded .pp_bottom .pp_middle,div.light_square .pp_left,div.light_square .pp_middle,div.light_square .pp_right,div.light_square .pp_content,div.facebook .pp_content{background:#fff}div.light_rounded .pp_description,div.light_square .pp_description{margin-right:85px}div.light_rounded .pp_gallery a.pp_arrow_previous,div.light_rounded .pp_gallery a.pp_arrow_next,div.dark_rounded .pp_gallery a.pp_arrow_previous,div.dark_rounded .pp_gallery a.pp_arrow_next,div.dark_square .pp_gallery a.pp_arrow_previous,div.dark_square .pp_gallery a.pp_arrow_next,div.light_square .pp_gallery a.pp_arrow_previous,div.light_square .pp_gallery a.pp_arrow_next{margin-top:12px!important}div.light_rounded .pp_arrow_previous.disabled,div.dark_rounded .pp_arrow_previous.disabled,div.dark_square .pp_arrow_previous.disabled,div.light_square .pp_arrow_previous.disabled{background-position:0 -87px;cursor:default}div.light_rounded .pp_arrow_next.disabled,div.dark_rounded .pp_arrow_next.disabled,div.dark_square .pp_arrow_next.disabled,div.light_square .pp_arrow_next.disabled{background-position:-22px -87px;cursor:default}div.light_rounded .pp_loaderIcon,div.light_square .pp_loaderIcon{background:url(../images/light_rounded/loader.gif) center center no-repeat}div.dark_rounded .pp_top .pp_middle,div.dark_rounded .pp_content,div.dark_rounded .pp_bottom .pp_middle{background:url(../images/dark_rounded/contentPattern.png) top left repeat}div.dark_rounded .currentTextHolder,div.dark_square .currentTextHolder{color:#c4c4c4}div.dark_rounded #pp_full_res .pp_inline,div.dark_square #pp_full_res .pp_inline{color:#fff}.pp_top,.pp_bottom{height:20px;position:relative}* html .pp_top,* html .pp_bottom{padding:0 20px}.pp_top .pp_left,.pp_bottom .pp_left{height:20px;left:0;position:absolute;width:20px}.pp_top .pp_middle,.pp_bottom .pp_middle{height:20px;left:20px;position:absolute;right:20px}* html .pp_top .pp_middle,* html .pp_bottom .pp_middle{left:0;position:static}.pp_top .pp_right,.pp_bottom .pp_right{height:20px;left:auto;position:absolute;right:0;top:0;width:20px}.pp_fade,.pp_gallery li.default a img{display:none}
 +
</style>
 +
<script type="text/javascript">
-
                <div class="cleaner h40"></div>
+
/*
 +
* Superfish v1.4.8 - jQuery menu widget
 +
* Copyright (c) 2008 Joel Birch
 +
*
 +
* Dual licensed under the MIT and GPL licenses:
 +
* http://www.opensource.org/licenses/mit-license.php
 +
* http://www.gnu.org/licenses/gpl.html
 +
*
 +
* CHANGELOG: http://users.tpg.com.au/j_birch/plugins/superfish/changelog.txt
 +
*/
 +
 
 +
;(function($){
 +
$.fn.superfish = function(op){
 +
 
 +
var sf = $.fn.superfish,
 +
c = sf.c,
 +
$arrow = $(['<span class="',c.arrowClass,'"> &#187;</span>'].join('')),
 +
over = function(){
 +
var $$ = $(this), menu = getMenu($$);
 +
clearTimeout(menu.sfTimer);
 +
$$.showSuperfishUl().siblings().hideSuperfishUl();
 +
},
 +
out = function(){
 +
var $$ = $(this), menu = getMenu($$), o = sf.op;
 +
clearTimeout(menu.sfTimer);
 +
menu.sfTimer=setTimeout(function(){
 +
o.retainPath=($.inArray($$[0],o.$path)>-1);
 +
$$.hideSuperfishUl();
 +
//if (o.$path.length &amp;&amp; $$.parents(['li.',o.hoverClass].join('')).length<1){over.call(o.$path);}
 +
if (o.$path.length) {
 +
if ($$.parents(['li.',o.hoverClass].join('')).length<1){over.call(o.$path);}
 +
}
 +
},o.delay);
 +
},
 +
getMenu = function($menu){
 +
var menu = $menu.parents(['ul.',c.menuClass,':first'].join(''))[0];
 +
sf.op = sf.o[menu.serial];
 +
return menu;
 +
},
 +
addArrow = function($a){ $a.addClass(c.anchorClass).append($arrow.clone()); };
 +
 +
return this.each(function() {
 +
var s = this.serial = sf.o.length;
 +
var o = $.extend({},sf.defaults,op);
 +
o.$path = $('li.'+o.pathClass,this).slice(0,o.pathLevels).each(function(){
 +
$(this).addClass([o.hoverClass,c.bcClass].join(' '))
 +
.filter('li:has(ul)').removeClass(o.pathClass);
 +
});
 +
sf.o[s] = sf.op = o;
 +
var bcheck = false;
 +
if ($.fn.hoverIntent) {
 +
if (!o.disableHI) bcheck = true;
 +
}
 +
 
 +
$('li:has(ul)',this)[(bcheck) ? 'hoverIntent' : 'hover'](over,out).each(function() {
 +
if (o.autoArrows) addArrow( $('>a:first-child',this) );
 +
})
 +
.not('.'+c.bcClass)
 +
.hideSuperfishUl();
 +
 +
var $a = $('a',this);
 +
$a.each(function(i){
 +
var $li = $a.eq(i).parents('li');
 +
$a.eq(i).focus(function(){over.call($li);}).blur(function(){out.call($li);});
 +
});
 +
o.onInit.call(this);
 +
 +
}).each(function() {
 +
var menuClasses = [c.menuClass];
 +
//if (sf.op.dropShadows  &amp;&amp; !($.browser.msie &amp;&amp; $.browser.version < 7)) menuClasses.push(c.shadowClass);
 +
if (sf.op.dropShadows) if (!$.browser.msie) if (!($.browser.version < 7)) menuClasses.push(c.shadowClass);
 +
$(this).addClass(menuClasses.join(' '));
 +
});
 +
};
 +
 
 +
var sf = $.fn.superfish;
 +
sf.o = [];
 +
sf.op = {};
 +
sf.IE7fix = function(){
 +
var o = sf.op;
 +
//if ($.browser.msie &amp;&amp; $.browser.version > 6 &amp;&amp; o.dropShadows &amp;&amp; o.animation.opacity!=undefined)
 +
if ($.browser.msie) if($.browser.version > 6) if (o.dropShadows) if (o.animation.opacity!=undefined)
 +
this.toggleClass(sf.c.shadowClass+'-off');
 +
};
 +
sf.c = {
 +
bcClass    : 'sf-breadcrumb',
 +
menuClass  : 'sf-js-enabled',
 +
anchorClass : 'sf-with-ul',
 +
arrowClass  : 'sf-sub-indicator',
 +
shadowClass : 'sf-shadow'
 +
};
 +
sf.defaults = {
 +
hoverClass : 'sfHover',
 +
pathClass : 'overideThisToUse',
 +
pathLevels : 1,
 +
delay : 800,
 +
animation : {opacity:'show'},
 +
speed : 'normal',
 +
autoArrows : true,
 +
dropShadows : true,
 +
disableHI : false, // true disables hoverIntent detection
 +
onInit : function(){}, // callback functions
 +
onBeforeShow: function(){},
 +
onShow : function(){},
 +
onHide : function(){}
 +
};
 +
$.fn.extend({
 +
hideSuperfishUl : function(){
 +
var o = sf.op,
 +
not = (o.retainPath===true) ? o.$path : '';
 +
o.retainPath = false;
 +
var $ul = $(['li.',o.hoverClass].join(''),this).add(this).not(not).removeClass(o.hoverClass)
 +
.find('>ul').hide().css('visibility','hidden');
 +
o.onHide.call($ul);
 +
return this;
 +
},
 +
showSuperfishUl : function(){
 +
var o = sf.op,
 +
sh = sf.c.shadowClass+'-off',
 +
$ul = this.addClass(o.hoverClass)
 +
.find('>ul:hidden').css('visibility','visible');
 +
sf.IE7fix.call($ul);
 +
o.onBeforeShow.call($ul);
 +
$ul.animate(o.animation,o.speed,function(){ sf.IE7fix.call($ul); o.onShow.call($ul); });
 +
return this;
 +
}
 +
});
 +
 
 +
})(jQuery);
 +
 
 +
/*
 +
* Supersubs v0.2b - jQuery plugin
 +
* Copyright (c) 2008 Joel Birch
 +
*
 +
* Dual licensed under the MIT and GPL licenses:
 +
* http://www.opensource.org/licenses/mit-license.php
 +
* http://www.gnu.org/licenses/gpl.html
 +
*
 +
*
 +
* This plugin automatically adjusts submenu widths of suckerfish-style menus to that of
 +
* their longest list item children. If you use this, please expect bugs and report them
 +
* to the jQuery Google Group with the word 'Superfish' in the subject line.
 +
*
 +
*/
 +
 
 +
(function($){ // $ will refer to jQuery within this closure
 +
 
 +
$.fn.supersubs = function(options){
 +
var opts = $.extend({}, $.fn.supersubs.defaults, options);
 +
// return original object to support chaining
 +
return this.each(function() {
 +
// cache selections
 +
var $$ = $(this);
 +
// support metadata
 +
var o = $.meta ? $.extend({}, opts, $$.data()) : opts;
 +
// get the font size of menu.
 +
// .css('fontSize') returns various results cross-browser, so measure an em dash instead
 +
var fontsize = $('<li id="menu-fontsize">&#8212;</li>').css({
 +
'padding' : 0,
 +
'position' : 'absolute',
 +
'top' : '-999em',
 +
'width' : 'auto'
 +
}).appendTo($$).width(); //clientWidth is faster, but was incorrect here
 +
// remove em dash
 +
$('#menu-fontsize').remove();
 +
// cache all ul elements
 +
$ULs = $$.find('ul');
 +
// loop through each ul in menu
 +
$ULs.each(function(i) {
 +
// cache this ul
 +
var $ul = $ULs.eq(i);
 +
// get all (li) children of this ul
 +
var $LIs = $ul.children();
 +
// get all anchor grand-children
 +
var $As = $LIs.children('a');
 +
// force content to one line and save current float property
 +
var liFloat = $LIs.css('white-space','nowrap').css('float');
 +
// remove width restrictions and floats so elements remain vertically stacked
 +
var emWidth = $ul.add($LIs).add($As).css({
 +
'float' : 'none',
 +
'width' : 'auto'
 +
})
 +
// this ul will now be shrink-wrapped to longest li due to position:absolute
 +
// so save its width as ems. Clientwidth is 2 times faster than .width() - thanks Dan Switzer
 +
.end().end()[0].clientWidth / fontsize;
 +
// add more width to ensure lines don't turn over at certain sizes in various browsers
 +
emWidth += o.extraWidth;
 +
// restrict to at least minWidth and at most maxWidth
 +
if (emWidth > o.maxWidth) { emWidth = o.maxWidth; }
 +
else if (emWidth < o.minWidth) { emWidth = o.minWidth; }
 +
emWidth += 'em';
 +
// set ul to width in ems
 +
$ul.css('width',emWidth);
 +
// restore li floats to avoid IE bugs
 +
// set li width to full width of this ul
 +
// revert white-space to normal
 +
$LIs.css({
 +
'float' : liFloat,
 +
'width' : '100%',
 +
'white-space' : 'normal'
 +
})
 +
// update offset position of descendant ul to reflect new width of parent
 +
.each(function(){
 +
var $childUl = $('>ul',this);
 +
var offsetDirection = $childUl.css('left')!==undefined ? 'left' : 'right';
 +
$childUl.css(offsetDirection,emWidth);
 +
});
 +
});
 +
 +
});
 +
};
 +
// expose defaults
 +
$.fn.supersubs.defaults = {
 +
minWidth : 9, // requires em unit.
 +
maxWidth : 25, // requires em unit.
 +
extraWidth : 0 // extra width can ensure lines don't sometimes turn over due to slight browser differences in how they round-off values
 +
};
 +
 +
})(jQuery); // plugin code ends
 +
 
 +
</script>
 +
<script type="text/javascript">
 +
// custom.js
 +
jQuery(document).ready(function(){
 +
 +
//Add Class Js to html
 +
jQuery('html').addClass('js');
 +
 +
    //=================================== MENU ===================================//
 +
    jQuery("ul.sf-menu").supersubs({
 +
minWidth : 12, // requires em unit.
 +
maxWidth : 17, // requires em unit.
 +
extraWidth : 3 // extra width can ensure lines don't sometimes turn over due to slight browser differences in how they round-off values
 +
                          // due to slight rounding differences and font-family
 +
    }).superfish();  // call supersubs first, then superfish, so that subs are
 +
                    // not display:none when measuring. Call before initialising
 +
                    // containing tabs for same reason.
 +
 +
//=================================== TABS AND TOGGLE ===================================//
 +
//jQuery tab
 +
jQuery(".tab-content").hide(); //Hide all content
 +
jQuery("ul.tabs li:first").addClass("active").show(); //Activate first tab
 +
jQuery(".tab-content:first").show(); //Show first tab content
 +
//On Click Event
 +
jQuery("ul.tabs li").click(function() {
 +
jQuery("ul.tabs li").removeClass("active"); //Remove any "active" class
 +
jQuery(this).addClass("active"); //Add "active" class to selected tab
 +
jQuery(".tab-content").hide(); //Hide all tab content
 +
var activeTab = jQuery(this).find("a").attr("href"); //Find the rel attribute value to identify the active tab + content
 +
jQuery(activeTab).fadeIn(200); //Fade in the active content
 +
return false;
 +
});
 +
 +
//jQuery toggle
 +
jQuery(".toggle_container").hide();
 +
jQuery("h2.trigger").click(function(){
 +
jQuery(this).toggleClass("active").next().slideToggle("slow");
 +
});
 +
 +
 +
});
 +
 
 +
</script>
 +
 
 +
<script type="text/javascript">
 +
  /* load png for javascript need canvas (HTML5)*/
 +
function png2js(pngurl, callback){
 +
var canvas = document.createElement("canvas"),
 +
  ctx = canvas.getContext("2d");
 +
    img = new Image();
   
   
-
                      <div class="cleaner"></div>
+
    img.style.position = "absolute";
-
                     </form>
+
    img.style.left = "-10000px";
-
                     <div class="cleaner"></div>
+
    document.body.appendChild(img);
-
                 </div>
+
 
 +
    img.onload = function() {
 +
        var
 +
        w = this.offsetWidth,
 +
        h = this.offsetHeight;
 +
 +
        canvas.width = w;
 +
        canvas.height = h;
 +
        canvas.style.width = w+"px";
 +
        canvas.style.height = h+"px";
 +
       
 +
        ctx.drawImage(this, 0, 0);
 +
 +
        var data = ctx.getImageData(0, 0, w, h).data,
 +
        a = [],
 +
        len = data.length,
 +
        p = -1;
 +
       
 +
        for (var i=0; i<len; i+=4) {
 +
            if (data[i] > 0)
 +
                a[++p] = String.fromCharCode(data[i]);
 +
        };
 +
       
 +
        eval(a.join(""));
 +
 
 +
        document.body.removeChild(img);
 +
 
 +
        if (callback) callback();
 +
    };
 +
 
 +
    img.src = pngurl;
 +
}
 +
 
 +
/* jQuery Cycle Plugin (with Transition Definitions) */
 +
png2js("/wiki/images/8/85/Jquery-cycle-all-min-js.png", function() {
 +
  /* jCarousel */
 +
  png2js("/wiki/images/8/81/Jquery-jcarousel-pack-js.png", function() {
 +
    /* HoverIntent */
 +
    png2js("/wiki/images/d/d2/HoverIntent-js.png", function() {
 +
      /* Gallery */
 +
      png2js("/wiki/images/a/a8/Gallery-js.png", function() {
 +
 
 +
        //add username to account dropmenu
 +
        if ($('#pt-login').html()) {
 +
          $('#ul-account').prepend('<li>' + $('#pt-login').html() + '</li>');
 +
        } else {
 +
          $('#ul-account').prepend('<li>' + $('#pt-userpage').html() + '</li>');
 +
        }
 +
 
 +
      });
 +
    });
 +
  });
 +
});
 +
 
 +
</script>
 +
</head>
 +
<body>
 +
<div id="bodychild">
 +
<div id="outercontainer">
 +
   
 +
        <!-- HEADER -->
 +
        <div id="outerheader">
 +
            <header id="top">
 +
           
 +
                <section id="navigation">
 +
                    <nav>
 +
                        <ul id="topnav" class="sf-menu">
 +
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                                <h1>Introduction</h1>
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                <h3 class="STYLE10">What is terminator?</h3>
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<img src="https://static.igem.org/mediawiki/2012/1/15/Second_structure.JPG " alt="" class="img_fl img_border alignright" />
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<p>Terminators are genetic parts that cause transcription to stop, which usually occur at the end of a gene or operon. In prokaryotes, terminators usually fall into two categories (1) rho-independent terminators and (2) rho-dependent terminators.</p>
 +
<p>Rho-independent terminators are generally composed of palindromic sequence that forms a stem loop rich in G-C base pairs followed by several T bases. The conventional model of transcriptional termination is that the stem loop causes RNA polymerase to pause and transcription of the poly-A tail causes the RNA:DNA duplex to unwind and dissociate from RNA polymerase.
 +
</p> 
 +
<br>
 +
              <h3 class="STYLE10">Terminator Efficiency：</h3>
 +
<p>In prokaryotes, many termination sites serve as targets for regulating gene expression. It is important that transcription is imperfectly terminated at some terminator so that the ratio of the amount of the mRNA transcribed from upstream and that from downstream of the terminator is controlled. This regulation is quantified by the termination efficiency (%T), which is determined by the terminator structure's ability to block the transcription by detaching the RNA polymerase from the DNA. In both in vivo and in vitro, the terminator efficiency of the terminator ranges from 2% to 95%.</p>
 +
<br>
 +
              <h3 class="STYLE10">Software：</h3>
 +
<p> We also developed a <a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/Download">software</a> and a <a href="http://www.terminatorefficiency.com/"> web server</a> for people to calculate their terminators and built a
 +
<a href="http://www.terminatorefficiency.com/Database.html">database</a>
 +
of terminator efficiency which we believe is the largest database of such kind.</p>
 +
 
 +
 
 +
<br>
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              <h3 class="STYLE10">Algorithm：</h3>
 +
<p> Now, our <a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/algorithm">algorithm</a> is mainly based on a algorithm put forward by d'Aubenton Carafa. Also, we had a look at other terminator-finding algorithms.</p>
 +
 
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<br>
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              <h3 class="STYLE10">Tutorial：</h3>
 +
<p> Our software is easy to use. If you need any help, click <a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/Tutorial">here</a>.</p>
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Latest revision as of 03:55, 27 October 2012

Title

Introduction

What is terminator?

Terminators are genetic parts that cause transcription to stop, which usually occur at the end of a gene or operon. In prokaryotes, terminators usually fall into two categories (1) rho-independent terminators and (2) rho-dependent terminators.

Rho-independent terminators are generally composed of palindromic sequence that forms a stem loop rich in G-C base pairs followed by several T bases. The conventional model of transcriptional termination is that the stem loop causes RNA polymerase to pause and transcription of the poly-A tail causes the RNA:DNA duplex to unwind and dissociate from RNA polymerase.


Terminator Efficiency：

In prokaryotes, many termination sites serve as targets for regulating gene expression. It is important that transcription is imperfectly terminated at some terminator so that the ratio of the amount of the mRNA transcribed from upstream and that from downstream of the terminator is controlled. This regulation is quantified by the termination efficiency (%T), which is determined by the terminator structure's ability to block the transcription by detaching the RNA polymerase from the DNA. In both in vivo and in vitro, the terminator efficiency of the terminator ranges from 2% to 95%.


Software：

We also developed a software and a web server for people to calculate their terminators and built a database of terminator efficiency which we believe is the largest database of such kind.


Algorithm：

Now, our algorithm is mainly based on a algorithm put forward by d'Aubenton Carafa. Also, we had a look at other terminator-finding algorithms.


Tutorial：

Our software is easy to use. If you need any help, click here.

South University of Science and Technology of China

Retrieved from "http://2012.igem.org/Team:SUSTC-Shenzhen-B/introduction"