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Brief Bioinform:中科院北京生科院赵方庆团队发表环形非编码RNA识别新技术

2017-04-21 佚名 中国科学院北京生命科学研究院

近日,国际学术期刊Briefings in Bioinformatics发表了中国科学院北京生命科学研究院赵方庆团队题为“Circular RNA identification based on multiple seed matching”的最新研究成果。因为目前在环形RNA识别方面存在着假阳性率高、敏感度不够等问题,该团队研究并提出了全新的多重种子匹配算法及最大似然估计模型,可以精确识别环形R

近日,国际学术期刊Briefings in Bioinformatics发表了中国科学院北京生命科学研究院赵方庆团队题为“Circular RNA identification based on multiple seed matching”的最新研究成果。因为目前在环形RNA识别方面存在着假阳性率高、敏感度不够等问题,该团队研究并提出了全新的多重种子匹配算法及最大似然估计模型,可以精确识别环形RNA接头序列,以显着提升环形RNA的识别效率。

目前已有的环形RNA识别算法均基于对环形RNA接头序列的查找,可分为基于注释的算法以及从头预测的算法。然而,由于真核生物转录的复杂性及环形RNA分子的特殊性,以上两类识别算法均面临着灵敏度低、可靠性差、运算时间长或内存使用高等问题,其应用也因此受到限制。此外,对上述识别算法的评价体系却仍主要依赖模拟数据,难以对相关算法在真实转录数据中的表现进行客观衡量。

针对此现状,赵方庆团队提出基于多重种子匹配策略的算法,针对比对质量较低的基因组区域,按长度降序进行种子序列提取,并将之与前后侧翼基因组区域进行快速匹配。同时,建立了最大似然估计模型,判断该种子序列的真实来源,并排除来自线性转录本或剪接副产物的干扰,从而极大提高了环形RNA分子识别的精度。该研究摒弃了偏差较大的模拟数据评测方法,采用 RNase R降解前后真实转录数据的比对体系,对10种已有算法进行全面的评测比较。结果显示本研究建立的方法在包含灵敏度与可靠性在内的综合表现(F1得分)上具有明显的优势,其并行模式还可进一步提升运算速度及内存使用效率。该算法与此团队开发的CIRI, CIRI-AS等分析工具(Genome Biology, 2015; Nature Communications, 2016)实现无缝衔接,将进一步促进环形RNA组成及功能等方面的研究。

该工作由赵方庆课题组的研究生高远和张金阳完成,得到了国家自然科学基金委和中国科学院的经费支持。

原始出处:

Gao Y, Zhang J, Zhao F.Circular RNA identification based on multiple seed matching.Brief Bioinform. 2017 Feb 28

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    2018-01-03 d830384
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    2017-08-26 sunylz
  4. 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level=null, likeNumber=92, replyNumber=0, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=https://wx.qlogo.cn/mmopen/icyLhIGqru6gIknBJqfuPhQkEvDREF6S2vZq3ZIpUYjdqicKVoAWaJSGoe8xNvS6o6QpmOlh2AQ7xuUpj8NiaDjJJgjbc7Xj3T6/0, createdBy=1c242047915, createdName=daiyaozu, createdTime=Sat Apr 22 08:40:11 CST 2017, time=2017-04-22, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=189585, encodeId=f191189585fc, content=谢谢分享,学习, beContent=null, objectType=article, channel=null, level=null, likeNumber=83, replyNumber=0, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=https://wx.qlogo.cn/mmopen/NUyjXTCJjo6Nx0VGA4QMDzOP8oAgnV4h51EjSfehJ9QxyiaSmw8PB56BhY8KXFSxHCibXrzcy4abrzSibXQPxJ9kzrLcJyhhB8a/0, createdBy=1d3b1672603, createdName=明月清辉, createdTime=Sat Apr 22 08:17:13 CST 2017, time=2017-04-22, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=189551, encodeId=585818955147, content=值得学习分享, beContent=null, objectType=article, channel=null, level=null, likeNumber=0, replyNumber=0, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=https://wx.qlogo.cn/mmopen/iaqwic5175nrs2asVmGicNahCpBSxNUbSuA4vpeiazhWPdV79iaSIJsvMiaGECEouckrnOYc6073M9RbpNPL6qU9SdfB5BsicIqON4X/0, createdBy=f47f2017208, createdName=1e20390em99(暂无匿称), createdTime=Sat Apr 22 07:10:27 CST 2017, time=2017-04-22, status=1, ipAttribution=)]
    2017-10-11 gous
  5. 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  6. 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level=null, likeNumber=92, replyNumber=0, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=https://wx.qlogo.cn/mmopen/icyLhIGqru6gIknBJqfuPhQkEvDREF6S2vZq3ZIpUYjdqicKVoAWaJSGoe8xNvS6o6QpmOlh2AQ7xuUpj8NiaDjJJgjbc7Xj3T6/0, createdBy=1c242047915, createdName=daiyaozu, createdTime=Sat Apr 22 08:40:11 CST 2017, time=2017-04-22, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=189585, encodeId=f191189585fc, content=谢谢分享,学习, beContent=null, objectType=article, channel=null, level=null, likeNumber=83, replyNumber=0, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=https://wx.qlogo.cn/mmopen/NUyjXTCJjo6Nx0VGA4QMDzOP8oAgnV4h51EjSfehJ9QxyiaSmw8PB56BhY8KXFSxHCibXrzcy4abrzSibXQPxJ9kzrLcJyhhB8a/0, createdBy=1d3b1672603, createdName=明月清辉, createdTime=Sat Apr 22 08:17:13 CST 2017, time=2017-04-22, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=189551, encodeId=585818955147, content=值得学习分享, beContent=null, objectType=article, channel=null, level=null, likeNumber=0, replyNumber=0, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=https://wx.qlogo.cn/mmopen/iaqwic5175nrs2asVmGicNahCpBSxNUbSuA4vpeiazhWPdV79iaSIJsvMiaGECEouckrnOYc6073M9RbpNPL6qU9SdfB5BsicIqON4X/0, createdBy=f47f2017208, createdName=1e20390em99(暂无匿称), createdTime=Sat Apr 22 07:10:27 CST 2017, time=2017-04-22, status=1, ipAttribution=)]
    2017-04-22 三生有幸9135

    学习一下谢谢分享

    0

  7. 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attachment=null, authenticateStatus=null, createdAvatar=https://wx.qlogo.cn/mmopen/jW482SpianMayicTRbRZ5RzaiabIFicf63hKvVMjL6aJlx4yX4UcXmzX9DyibCRcicq0QtCRWMaQKh8MYjE1D3EKUBopgiaGWYuqbeR/0, createdBy=0c2b1999806, createdName=三生有幸9135, createdTime=Sat Apr 22 14:04:09 CST 2017, time=2017-04-22, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=189594, encodeId=f0f418959407, content=学习了很有用, beContent=null, objectType=article, channel=null, level=null, likeNumber=79, replyNumber=0, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=https://wx.qlogo.cn/mmopen/oLAjfB7s1ib3IzoRn621JdKCFUI4XvNELcibocrAVU6aUzEVDSaf3rYH08PUYUiagGqxAEhj8g9WqqNvD1CupIpCrmnR2OrqHZh/0, createdBy=7f181365728, createdName=飛歌, createdTime=Sat Apr 22 09:58:48 CST 2017, time=2017-04-22, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=189591, encodeId=5be7189591da, content=学习了,不错, beContent=null, objectType=article, channel=null, level=null, likeNumber=92, replyNumber=0, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=https://wx.qlogo.cn/mmopen/icyLhIGqru6gIknBJqfuPhQkEvDREF6S2vZq3ZIpUYjdqicKVoAWaJSGoe8xNvS6o6QpmOlh2AQ7xuUpj8NiaDjJJgjbc7Xj3T6/0, createdBy=1c242047915, createdName=daiyaozu, createdTime=Sat Apr 22 08:40:11 CST 2017, time=2017-04-22, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=189585, encodeId=f191189585fc, content=谢谢分享,学习, beContent=null, objectType=article, channel=null, level=null, likeNumber=83, replyNumber=0, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=https://wx.qlogo.cn/mmopen/NUyjXTCJjo6Nx0VGA4QMDzOP8oAgnV4h51EjSfehJ9QxyiaSmw8PB56BhY8KXFSxHCibXrzcy4abrzSibXQPxJ9kzrLcJyhhB8a/0, createdBy=1d3b1672603, createdName=明月清辉, createdTime=Sat Apr 22 08:17:13 CST 2017, time=2017-04-22, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=189551, encodeId=585818955147, content=值得学习分享, beContent=null, objectType=article, channel=null, level=null, likeNumber=0, replyNumber=0, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=https://wx.qlogo.cn/mmopen/iaqwic5175nrs2asVmGicNahCpBSxNUbSuA4vpeiazhWPdV79iaSIJsvMiaGECEouckrnOYc6073M9RbpNPL6qU9SdfB5BsicIqON4X/0, createdBy=f47f2017208, createdName=1e20390em99(暂无匿称), createdTime=Sat Apr 22 07:10:27 CST 2017, time=2017-04-22, status=1, ipAttribution=)]
    2017-04-22 飛歌

    学习了很有用

    0

  8. 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level=null, likeNumber=92, replyNumber=0, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=https://wx.qlogo.cn/mmopen/icyLhIGqru6gIknBJqfuPhQkEvDREF6S2vZq3ZIpUYjdqicKVoAWaJSGoe8xNvS6o6QpmOlh2AQ7xuUpj8NiaDjJJgjbc7Xj3T6/0, createdBy=1c242047915, createdName=daiyaozu, createdTime=Sat Apr 22 08:40:11 CST 2017, time=2017-04-22, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=189585, encodeId=f191189585fc, content=谢谢分享,学习, beContent=null, objectType=article, channel=null, level=null, likeNumber=83, replyNumber=0, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=https://wx.qlogo.cn/mmopen/NUyjXTCJjo6Nx0VGA4QMDzOP8oAgnV4h51EjSfehJ9QxyiaSmw8PB56BhY8KXFSxHCibXrzcy4abrzSibXQPxJ9kzrLcJyhhB8a/0, createdBy=1d3b1672603, createdName=明月清辉, createdTime=Sat Apr 22 08:17:13 CST 2017, time=2017-04-22, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=189551, encodeId=585818955147, content=值得学习分享, beContent=null, objectType=article, channel=null, level=null, likeNumber=0, replyNumber=0, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=https://wx.qlogo.cn/mmopen/iaqwic5175nrs2asVmGicNahCpBSxNUbSuA4vpeiazhWPdV79iaSIJsvMiaGECEouckrnOYc6073M9RbpNPL6qU9SdfB5BsicIqON4X/0, createdBy=f47f2017208, createdName=1e20390em99(暂无匿称), createdTime=Sat Apr 22 07:10:27 CST 2017, time=2017-04-22, status=1, ipAttribution=)]
    2017-04-22 daiyaozu

    学习了,不错

    0

  9. 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level=null, likeNumber=92, replyNumber=0, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=https://wx.qlogo.cn/mmopen/icyLhIGqru6gIknBJqfuPhQkEvDREF6S2vZq3ZIpUYjdqicKVoAWaJSGoe8xNvS6o6QpmOlh2AQ7xuUpj8NiaDjJJgjbc7Xj3T6/0, createdBy=1c242047915, createdName=daiyaozu, createdTime=Sat Apr 22 08:40:11 CST 2017, time=2017-04-22, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=189585, encodeId=f191189585fc, content=谢谢分享,学习, beContent=null, objectType=article, channel=null, level=null, likeNumber=83, replyNumber=0, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=https://wx.qlogo.cn/mmopen/NUyjXTCJjo6Nx0VGA4QMDzOP8oAgnV4h51EjSfehJ9QxyiaSmw8PB56BhY8KXFSxHCibXrzcy4abrzSibXQPxJ9kzrLcJyhhB8a/0, createdBy=1d3b1672603, createdName=明月清辉, createdTime=Sat Apr 22 08:17:13 CST 2017, time=2017-04-22, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=189551, encodeId=585818955147, content=值得学习分享, beContent=null, objectType=article, channel=null, level=null, likeNumber=0, replyNumber=0, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=https://wx.qlogo.cn/mmopen/iaqwic5175nrs2asVmGicNahCpBSxNUbSuA4vpeiazhWPdV79iaSIJsvMiaGECEouckrnOYc6073M9RbpNPL6qU9SdfB5BsicIqON4X/0, createdBy=f47f2017208, createdName=1e20390em99(暂无匿称), createdTime=Sat Apr 22 07:10:27 CST 2017, time=2017-04-22, status=1, ipAttribution=)]
    2017-04-22 明月清辉

    谢谢分享,学习

    0

  10. 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level=null, likeNumber=92, replyNumber=0, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=https://wx.qlogo.cn/mmopen/icyLhIGqru6gIknBJqfuPhQkEvDREF6S2vZq3ZIpUYjdqicKVoAWaJSGoe8xNvS6o6QpmOlh2AQ7xuUpj8NiaDjJJgjbc7Xj3T6/0, createdBy=1c242047915, createdName=daiyaozu, createdTime=Sat Apr 22 08:40:11 CST 2017, time=2017-04-22, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=189585, encodeId=f191189585fc, content=谢谢分享,学习, beContent=null, objectType=article, channel=null, level=null, likeNumber=83, replyNumber=0, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=https://wx.qlogo.cn/mmopen/NUyjXTCJjo6Nx0VGA4QMDzOP8oAgnV4h51EjSfehJ9QxyiaSmw8PB56BhY8KXFSxHCibXrzcy4abrzSibXQPxJ9kzrLcJyhhB8a/0, createdBy=1d3b1672603, createdName=明月清辉, createdTime=Sat Apr 22 08:17:13 CST 2017, time=2017-04-22, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=189551, encodeId=585818955147, content=值得学习分享, beContent=null, objectType=article, channel=null, level=null, likeNumber=0, replyNumber=0, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=https://wx.qlogo.cn/mmopen/iaqwic5175nrs2asVmGicNahCpBSxNUbSuA4vpeiazhWPdV79iaSIJsvMiaGECEouckrnOYc6073M9RbpNPL6qU9SdfB5BsicIqON4X/0, createdBy=f47f2017208, createdName=1e20390em99(暂无匿称), createdTime=Sat Apr 22 07:10:27 CST 2017, time=2017-04-22, status=1, ipAttribution=)]
    2017-04-22 1e20390em99(暂无匿称)

    值得学习分享

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