云之南

风声，雨声，读书声，声声入耳；家事，国事，天下事，事事关心

日志

关于我

云之南

专业背景：计算机科学研究方向与兴趣: JavaEE-Web软件开发, 生物信息学, 数据挖掘与机器学习, 智能信息系统目前工作: 基因组, 转录组, NGS高通量数据分析, 生物数据挖掘, 植物系统发育和比较进化基因组学

文章分类

miRNA靶基因预测软件

2011-06-01 14:51:32| 分类： noncodingRNA | 标签： |举报 |字号大中小订阅

下载LOFTER 我的照片书 |

?miRanda 脊椎动物 http://www.microrna.org/

DIANA-microT 所有哺乳动物 http://www.diana.pcbi.upenn.edu/

RNAhybrid 所有哺乳动物 http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/

TargetScan 脊椎动物 http://www.targetscan.org/

MicroInspector 所有哺乳动物 http://mirna.imbb.forth.gr/microinspector/

PicTar 所有哺乳动物 http://pictar.bio.nyu.edu/

TargetBoost 线虫和果蝇 https://demo1.interagon.com/targetboost/

miTarget 所有哺乳动物 http://cbit.snu.ac.kr/~miTarget/

RNA22 所有哺乳动物 http://cbcsrv.watson.ibm.com/rna22.html

microTar 线虫、果蝇和小鼠 http://tiger.dbs.nus.edu.sg/microtar/

植物：
psRNATarget
http://plantgrn.noble.org/psRNATarget/

PAREsnip:
http://srna-workbench.cmp.uea.ac.uk/tools/paresnip/

SoMART, the Server for plant miRNA/tasiRNA Analysis Resources and Tools
http://somart.ist.berkeley.edu/

【转】microRNA Target Prediction Tools

http://mirnablog.com/microrna-target-prediction-tools/

miRecords is resource for animal miRNA-target interactions developed at the University of Minnesota. miRecords consists of two components. The Validated Targets component is a large, high-quality database of experimentally validated miRNA targets resulting from meticulous literature curation. The Predicted Targets component of miRecords is an integration of predicted miRNA targets produced by 11 established miRNA target prediction programs

PicTar is an algorithm for the identification of microRNA targets. This searchable website provides details (3′ UTR alignments with predicted sites, links to various public databases etc) regarding microRNA target predictions in vertebrates, several Drosophila species, and C. elegans.

miRanda is an algorithm for finding genomic targets for microRNAs. This algorithm has been written in C and is available as an open-source method under the GPL. MiRanda was developed at the Computational Biology Center of Memorial Sloan-Kettering Cancer Center. This software will be further developed under the open source model, coordinated by Anton Enright and Chris Sander (miranda@cbio.mskcc.org).

TargetScan: Prediction of microRNA targets – These are the most recent TargetScanS predictions (April 2005). They are essentially the 3′UTR targets reported in the Lewis et al., 2005 paper, with a few changes arising from updated gene boundary definitions from the April 2005 UCSC genome browser mapping of RefSeq mRNAs to the hg17 human genome assembly. To avoid difficulties in browser display, the few predictions spanning splice junctions are excluded.

RNAhybrid is a tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, ie. the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction.

miRNA – Target Gene Prediction at EMBL – This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs. Both methods make use of genome comparison across insect species. Our 2005 predictions are based on pairing rules from a systematic experimental study (Brennecke & Stark et al., 2005) and have a very high sensitivity and specificity as assessed by experimental tests (see Supplement in Stark & Brennecke et al., 2005). We thus highly recommend to use the new predictions.

DIANA MicroT Analyzer – A tool for prediction of MicroRNA targets

RegRNA – is an integrated web server for identifying the homologs of Regulatory RNA motifs and elements against an input mRNA sequence. Both sequence homologs or structural homologs of regulatory RNA motifs can be identified.

MicroInspector – A scanning software for detection of microRNA binding sites.

RNA22 – A pattern-based method for the identification of microRNA-target sites and their corresponding RNA/RNA complexes.

TargetBoost – MicroRNA target prediction demo.

psRNATarget: A Plant Small RNA Target Analysis Server – A plant small RNA (including microRNAs) target analysis server, which features two important analysis functions: 1) reverse complementary matching between miRNA and target transcript using a proven scoring schema, and 2) target site accessibility evaluation by calculating unpaired energy (UPE) required to “open” secondary structure around miRNA’s target site on mRNA. PsRNATarget incorporates recent discoveries in plant miRNA target recognition, e.g. it distinguishes translational and post-transcriptional inhibition, and it reports the number of miRNA/target site pairs that may affect miRNA binding activity to target transcript. psRNA Target is replacing miRU (Plant microRNA Potential Target Finder) by the same group.

Incoming search terms for this article:

评论这张

转发至微博

阅读(6259)| 评论(2)

历史上的今天

this.p={  m:2,
              b:2,
              loftPermalink:'',
              id:'fks_095064084082087074092094085095085094087074093087083071',
              blogTitle:'miRNA靶基因预测软件',
              blogAbstract:'<p\><wbr\>?miRanda 脊椎动物  <a rel=\"nofollow\" href=\"http://www.microrna.org/\"  \>http://www.microrna.org/</a\> </p\>  <p\>DIANA-microT 所有哺乳动物  <a rel=\"nofollow\" href=\"http://www.diana.pcbi.upenn.edu/\"  \>http://www.diana.pcbi.upenn.edu/</a\>  </p\>  <p\><br\>RNAhybrid 所有哺乳动物  <a rel=\"nofollow\" href=\"http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/\"  \>http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/</a\> </p\>  <p\><br\>TargetScan 脊椎动物  <a rel=\"nofollow\" href=\"http://www.targetscan.org/\"  \>http://www.targetscan.org/</a\> </p\>  <p\><br\>MicroInspector 所有哺乳动物  </p\>',
              blogTag:'',
              blogUrl:'blog/static/1869915420115125132246',
              isPublished:1,
              istop:false,
              type:0,
              modifyTime:1337830726946,
              publishTime:1306911092246,
              permalink:'blog/static/1869915420115125132246',
              commentCount:2,
              mainCommentCount:2,
              recommendCount:1,
              bsrk:-100,
              publisherId:0,
              recomBlogHome:false,
              currentRecomBlog:false,
              attachmentsFileIds:[],
              vote:{},
              groupInfo:{},
              friendstatus:'none',
              followstatus:'unFollow',
              pubSucc:'',
              visitorProvince:'',
              visitorCity:'',
              visitorNewUser:false,
              postAddInfo:{},
              mset:'000',
              mcon:'',
              srk:-100,
              remindgoodnightblog:false,
              isBlackVisitor:false,
              isShowYodaoAd:true,
              hostIntro:'专业背景：计算机科学                           \n\n研究方向与兴趣: JavaEE-Web软件开发,\n生物信息学, 数据挖掘与机器学习, 智能信息系统                                                                \n目前工作: 基因组, 转录组, NGS高通量数据分析, 生物数据挖掘, 植物系统发育和比较进化基因组学',
              hmcon:'1',
              selfRecomBlogCount:'0',
              lofter_single:'<iframe width="140" height="560" style="overflow:hidden;" src="http://www.lofter.com/mailEntry.do?blogad=1&blog" frameBorder="0"></iframe>'
            }

{list a as x}
    {if !!x}
    <div class="iblock nbw-fce nbw-f40">
      <a class="fc03 noul" target="_blank" hidefocus="true" href="http://blog.163.com/${x.visitorName}/">
      {if x.visitorName==visitor.userName}
      <img alt="${x.visitorNickname|escape}" onerror="this.src=location.f40" class="cwd bdwa bdc0" src="${fn1(x.visitorName)}&r=${visitor.imageUpdateTime}"/>
      {else}
      <img alt="${x.visitorNickname|escape}" onerror="this.src=location.f40" class="cwd bdwa bdc0" src="${fn1(x.visitorName)}"/>
      {/if}
      </a>
      <div class="cwd vname thide">
        {if x.moveFrom=='wap'}
          <a class="noul pnt" target="_blank" href="http://blog.163.com/services/wapblog.html?frompersonalbloghome"><span title="来自网易手机博客" class="iblock wapIcon"> </span></a>
        {elseif x.moveFrom=='iphone'}
          <a class="noul pnt" target="_blank"><span title="来自iPhone客户端" class="iblock iphoneIcon"> </span></a>
        {elseif x.moveFrom=='android'}
          <a class="noul pnt" target="_blank"><span title="来自Android客户端" class="iblock androidIcon"> </span></a>
        {elseif x.moveFrom=='mobile'}
          <a class="noul pnt" target="_blank" href="http://blog.163.com/services/emsblog.html?frompersonalbloghome"><span title="来自网易短信写博" class="iblock wapIcon"> </span></a>
        {/if}
        <a class="fc03 m2a"  target="_blank" hidefocus="true" href="http://blog.163.com/${x.visitorName}/">
          ${fn(x.visitorNickname,8)|escape}
        </a>
      </div>
    </div>
    {/if}
    {/list}

<#--最新日志，群博日志--> <#--推荐日志-->

<p class="fc06">推荐过这篇日志的人：</p>
    <div>
      {list a as x}
      {if !!x}
      <div class="iblock nbw-fce nbw-f40">
        <a class="fc03 noul" target="_blank" hidefocus="true" href="http://blog.163.com/${x.recommenderName}/">
        <img alt="${x.recommenderNickname|escape}" onerror="this.src=location.f40" class="cwd bdwa bdc0" src="${fn1(x.recommenderName)}"/>
        </a>
        <div class="cwd thide">
          <a class="fc03 m2a" target="_blank" hidefocus="true" href="http://blog.163.com/${x.recommenderName}/">
            ${fn(x.recommenderNickname,6)|escape}
          </a>
        </div>
      </div>
      {/if}
      {/list}
    </div>
    {if !!b&&b.length>0}
    <p  class="fc06">他们还推荐了：</p>
    <ul>
    {list b as y}
      {if !!y}
        <li class="rrb"><span class="iblock">·</span><a class="fc03 m2a" target="_blank" href="http://blog.163.com/${y.recommendBlogPermalink}/?from=blog/static/1869915420115125132246">${y.recommendBlogTitle|escape}</a></li>
      {/if}
    {/list}
    </ul>
    {/if}

<#--引用记录--> <#--博主推荐--> <#--随机阅读--> <#--首页推荐--> <#--历史上的今天--> <#--被推荐日志--> <#--上一篇，下一篇--> <#-- 热度 -->

{list a as x}
    {if !!x}
    <div class="hotItem iblock nbw-fce nbw-f40">
      <a class="fc03 noul" target="_blank" hidefocus="true" href="http://blog.163.com/${x.publisherUsername}/">
      {if x.publisherUsername==visitor.userName}
      <img alt="${x.publisherNickname|escape}" onerror="this.src=location.f40" class="cwd bdwa bdc0" src="${fn1(x.publisherUsername)}&r=${visitor.imageUpdateTime}"/>
      {else}
      <img alt="${x.publisherNickname|escape}" onerror="this.src=location.f40" class="cwd bdwa bdc0" src="${fn1(x.publisherUsername)}"/>
      {/if}
      </a>
      <div class="cwd vname thide">
        <a class="fc03 m2a"  target="_blank" hidefocus="true" href="http://blog.163.com/${x.publisherUsername}/">
          ${fn(x.publisherNickname,8)|escape}
        </a>
      </div>
      <a class="f-myLikeIcons hottype {if x.type==1} js-liketype{elseif x.type==2} js-reblogtype{elseif x.type==3} js-sharetype{else}{/if}" target="_blank" hidefocus="true" href="http://blog.163.com/${x.publisherUsername}/"> </a>
    </div>
    {/if}
    {/list}

<#-- 网易新闻广告 --> <#--右边模块结构--> <#--评论模块结构--> <#--引用模块结构--> <#--博主发起的投票-->

页脚

我的照片书 - 手机博客 - 下载LOFTER APP - 订阅此博客

云之南

导航

日志

miRNA靶基因预测软件

【转】microRNA Target Prediction Tools

Incoming search terms for this article:

历史上的今天

最近读者

热度

评论

页脚