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1.mirspongeÊý¾Ý¿â:http://www.bio-bigdata.com/mirsponge/
2.rna22ÍøÕ¾:https://cm.jefferson.edu/rna22/
3.lncactdbÊý¾Ý¿â:http://www.bio-bigdata.net/lncactdb/
4.raid v2.0Êý¾Ý¿â:http://www.rna-society.org/raid/index.html
5.diana toolsÊý¾Ý¿â:http://carolina.imis.athena-inno ... p?r=lncbasev2/index
6.starbaseÊý¾Ý¿â:http://starbase.sysu.edu.cn/index.php
7.mircodeÊý¾Ý¿âhttp://www.mircode.org/
8. lnceditingÊý¾Ý¿âhttp://bioinfo.life.hust.edu.cn/lncediting/
9.lncrnasnpÊý¾Ý¿âhttp://bioinfo.life.hust.edu.cn/lncrnasnp/(¿ÉÒÔÔ¤²âÈË,СÊó)
10.lncrnamapÊý¾Ý¿âhttp://lncrnamap.mbc.nctu.edu.tw/php/
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1. targetscan
targetscanÊý¾Ý¿âÊÇ´ó¼Ò±È½Ï³£ÓõÄÔ¤²âmirna°Ð»ùÒòÊý¾Ý¿â,Ö÷Ҫͨ¹ýËÑË÷ºÍÿÌõmirnaÖÖ×ÓÇøÓòÆ¥ÅäµÄ±£ÊصÄ8merºÍ7merλµãÀ´Ô¤²â°Ð»ùÒò¡£¸ÃÊý¾Ý¿âÌṩÈË¡¢Ð¡Êó¡¢´óÊó¡¢ÄÌÅ£¡¢¹·¡¢ÐÉÐÉ¡¢ºãºÓºï¡¢¸ºÊó¡¢¼¦ºÍÇàÍܵȶ¯ÎïÐÅÏ¢¡£×îиüÐÂʱ¼äΪ2015Äê8ÔÂ,°æ±¾Îªv7.0¡£Á´½Ó:http://www.targetscan.org/
2.pita
¸ÃÊý¾Ý¿â»ùÓÚ°ÐλµãµÄ¿É½ÓÐÔ(target-site accessibility)ºÍ×ÔÓÉÄÜÔ¤²âmirna µÄ°Ð±ê,ÊÇÖøÃûµÄÉúÎïÐÅϢѧ¼ÒsegalʵÑéÊÒ¿ª·¢µÄ¡£Ö÷Òª°üº¬human¡¢mouse¡¢flyºÍwormµÄÐÅÏ¢,ʹÓÃÕß¿ÉÒÔͨ¹ýmirnaÔ¤²â°Ð»ùÒò,Ò²¿ÉÒÔͨ¹ýmrnaÔ¤²âmirnaÐÅÏ¢,ÎÞÂÛÊÇmirna»¹ÊÇmrna¾ù¿Éͨ¹ýÌṩname»òid½øÐзÖÎö¡£Á´½Ó:http://genie.weizmann.ac.il/pubs/mir07/mir07_dyn_data.html
3.mirbase
mirbaseÊý¾Ý¿âÊÇÒ»¸öÌṩ°üÀ¨ÒÑ·¢±íµÄmirnaÐòÁÐÊý¾Ý¡¢×¢ÊÍ¡¢Ô¤²â»ùÒò°Ð±êµÈÐÅÏ¢µÄÈ«·½Î»Êý¾Ý¿â,ÊÇ´æ´¢mirnaÐÅÏ¢×îÖ÷ÒªµÄ¹«¹²Êý¾Ý¿âÖ®Ò»¡£¸ÃÊý¾Ý¿âÓÚ2014Äê6Ô¸üÐÂΪ×îа汾v21.0,°üº¬223¸öÎïÖÖµÄ35828¸ö³ÉÊìµÄmirnaÐòÁС£¸ÃÊý¾Ý¿âÌṩ±ã½ÝµÄÍøÉϲéѯ·þÎñ,ÔÊÐíÓû§Ê¹Óùؼü´Ê»òÐòÁÐÔÚÏßËÑË÷ÒÑÖªµÄmirnaºÍ°Ð±êÐÅÏ¢(½ö°üº¬ÒÑÓеİбêÐÅÏ¢,ËùÒÔ»á³öÏÖ²¿·Ömirna°Ð±êÐÅÏ¢ÎÞµÄÏÖÏó)¡£¸ÃÊý¾Ý¿âÓÃÓÚmirnaÐÅÏ¢²éѯ½Ï¶à,°Ð¹ØϵԤ²â½ÏÉÙ¡£Á´½Ó:http://www.mirbase.org/
4.microra.org
¸ÃÊý¾Ý¿âÌṩÁ˹ØÓÚÈËÀࡢСÊó¡¢´óÊó¡¢¹ûÓ¬ºÍ°ßÂíÓã»ùÒò×éµÄmicrorna°ÐÄ¿±êµÄÔ¤²âÐÅÏ¢ÒÔ¼°mirnaÔÚ²»Í¬×éÖ¯µÄ±í´ïÆ×,Ö§³Öͨ¹ýmirnaÔ¤²â°Ð»ùÒò,Ò²Ö§³Öͨ¹ýmrna·ÖÎöÏà¹ØµÄmirna¡£×îиüÐÂʱ¼äΪ2010Äê,ºÃ¾Ã²»¸üÐÂÁË¡£Á´½Ó:http://www.microrna.org/
5.mirtarbase
¸ÃÊý¾Ý¿âÖ÷ÒªÊÕ¼¯µÄÊDZ»ÊµÑéÑéÖ¤µÄmirna°Ð±ê,ͬʱÌṩ֧³ÖËÑË÷½á¹ûµÄÎÄÏ×»ò·½·¨,×îиüÐÂÓÚ2015Äê9Ô¡£¸ÃÊý¾Ý¿âÖ§³Öä¯ÀÀ¡¢ËÑË÷ºÍÊý¾ÝÏÂÔØ¡£Á´½Ó:http://mirtarbase.mbc.nctu.edu.tw/
6.starbase v2.0
¸ÃÊý¾Ý¿â²É¼¯ÁË6000¶à·ÝÑù±¾,14ÖÖ°©Ö¢À´×ÔÓÚ37¸ö¶ÀÁ¢Ñо¿µÄ108·Ýclip-seqÊý¾Ý,ͬʱ¸¨Öú½µ½â×éʵÑéÊý¾ÝËÑÑ°mirnaµÄ°Ð±ê,ÌṩÁ˸÷ʽ¸÷ÑùµÄ¿ÉÊÓ»¯½çÃæȥ̽ÌÖmirna°Ð±ê¡£³ýÁËmirnaºÍ°Ð±êmrnaÖ®¼ä¹Øϵ,¸ÃÊý¾Ý¿â»¹½øÐÐlncrna¡¢circrna¡¢proteinÓëmrnaÖ®¼äµÄÏ໥×÷Ó÷ÖÎö,²¢·ÖÎöÁËcerna»úÖÆ¡£¸ÃÊý¾Ý¿âÖ÷Òª°üº¬ÈË¡¢Ð¡Êó¡¢Ïß³æ3¸öÎïÖÖÐÅÏ¢¡£Á´½Ó:http://starbase.sysu.edu.cn/
Èý¡¢mirnaÏà¹ØÊý¾Ý¿â
1.evmirna (http://bioinfo.life.hust.edu.cn/evmirna),ÌṩÈý¸ö¹¦ÄÜÄ£¿éi)mirna±í´ïÆ׺ÍÀ´×Ô²»Í¬À´Ô´(ÀýÈçѪҺ¡¢Ä¸ÈéµÈ)µÄevµÄÑùÆ·ÐÅÏ¢;(ii)²»Í¬evÖÐÌØÒìÐÔ±í´ïµÄmirna,ÓÐÖúÓÚÉúÎï±êÖ¾Îï¼ø¶¨;(iii)mirna×¢ÊÍ,°üÀ¨evºÍtcga°©Ö¢ÀàÐÍÖеÄmirna±í´ï,mirnaͨ·µ÷½ÚÒÔ¼°mirna¹¦Äܺͳö°æÎï¡£evmirna¾ßÓÐÓû§ÓѺõÄweb½çÃæ,¾ßÓÐÇ¿´óµÄä¯ÀÀºÍËÑË÷¹¦ÄÜ,ÒÔ¼°Êý¾ÝÏÂÔØ¡£ËüÊǵÚÒ»¸öרעÓÚevÖÐmirna±í´ïÆ×µÄÊý¾Ý¿â,¿ÉÓÃÓÚevÉúÎï±êÖ¾Îï¡¢mirna¹¦ÄܺÍÒºÌå»î¼ìµÄÑо¿ºÍÓ¦ÓÃÁìÓò¡£
2.mir2disease (http://www.mir2disease.org/)Ò»¸öÊÖ¹¤´òÔìµÄÊý¾Ý¿â,Ö¼ÔÚÌṩһ¸öÈ«ÃæµÄmicrorna¶ÔÓ¦¸÷ÖÖÈËÀ༲²¡µÄ×ÊÔ´¡£ÆäÖеÄÿ¸öÌõÄ¿°üº¬mirna-disease¹ØϵµÄÏêϸÐÅÏ¢,°üÀ¨micrornaµÄid¡¢¼²²¡Ãû³Æ¡¢mirna-disease¹ØϵµÄ¼òÒªÃèÊö¡¢micrornaÔÚ²»Í¬¼²²¡×´Ì¬µÄ±í´ïģʽ¡¢micrornaµÄ±í´ï¼ì²â·½·¨¡¢Í¨¹ýʵÑéÑéÖ¤micrornaµÄÄ¿±ê»ùÒòºÍ²Î¿¼ÎÄÏס£
3.mirwalk (http://zmf.umm.uni-heidelberg.de/apps/zmf/mirwalk/ )²éÕÒͨ·ÖеÄmirnaÒÔ¼°Æä°Ð»ùÒò,²¢ÇÒÄܹ»²éѯ¼²²¡Ïà¹Ømirna¡£
4.hmdd (http://www.cuilab.cn/hmdd )ÌṩÓë¼²²¡Ïà¹ØµÄmirnaÒÔ¼°Æä°Ð»ùÒò,ÔÚͨ··ÖÎöµÄʱºò½âÁÐmirwalk·Ç³£ÓÐÓá£
5¡¢diana (http://diana.imis.athena-innovation.gr/dianatools/index. php?r=site/page&view=software )ÕâÊǷdz£×ۺϵĹØÓÚmirna·ÖÎöµÄ¹¤¾ß³§¡£
6¡¢cogemir(http://cogemir.tigem.it/)
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1.silva(https://www.arb-silva.de/)ÊÇÒ»¸öº¸Çϸ¾ú¡¢¹Å¾ú¡¢ÕæºËµÄrrna»ùÒòÐòÁеÄ×ÛºÏÊý¾Ý¿â
2.pr2(https://www.researchgate.net/pro ... r2(protistribosomal reference database)Êý¾Ý¿âÊÇרÃÅÕë¶ÔÕæºË΢ÉúÎïСÑÇ»ùssu rrna(¼´18srrna)»ùÒòµÄÊý¾Ý¿â¡£¸ÃÊý¾Ý¿âÖ÷ÒªÓɺ˱àÂëµÄÔÉúÉúÎïÐòÁй¹³É,µ«Îª·½±ã·ÖÎö18sµÄ¸ßͨÁ¿²âÐòÊý¾Ý,Êý¾Ý¿âÒ²°üº¬Á˺óÉúÉúÎ½µØÖ²Îï¡¢´óÐÍÕæ¾úºÍÕæºËϸ°ûÆ÷(ÏßÁ£Ìå¡¢ÖÊÌåµÈ)µÄssuÐòÁС£ÄÚº¬×ÓºÍǶºÏÌåÐòÁÐÒѱ»È¥³ý¡£ÏÖpr2Ö÷Ò³Òò¼¼Êõ¹ÊÕÏÎÞ·¨µÇ½,µ«ÊÇÊý¾Ý¿âÒ»Ö±ÔÚ¸üÐÂ,×îÐÂÊý¾Ý¿ÉÔÚhttps://figshare.com/articles/pr2_rrna_gene_database/3803709ÏÂÔØ¡£
3.rdp (http://rdp.cme.msu.edu/index.jsp) rdpÊý¾Ý¿âÈ«³Æ¡°ribosomaldatabase project¡±,¸ÃÊý¾Ý¿âÌṩÖÊ¿Ø¡¢±È¶Ô¡¢×¢Ê͵Äϸ¾ú¡¢¹Å¾ú16s rrna»ùÒòºÍÕæ¾ú28s rrna»ùÒòÐòÁС£rdpÊÇÄ¿Ç°½Ï³£ÓõÄrrna»ùÒò¸ßͨÁ¿²âÐòºó×÷Ϊ±È¶Ô¡¢×¢Ê͵IJο¼Êý¾Ý¿â¡£´ËÍâ,»¹¿ÉÓÃÓÚƽʱ¾úÖÖ¼ø¶¨Ê±,¶ÔÉÙÁ¿rrna»ùÒò²âÐòºóµÄÎïÖÖ½øÐзÖÀà¼ø¶¨,´ËʱÖ÷ÒªÓÃÆäclassifier¹¦ÄÜ(http://rdp.cme.msu.edu/classifier /classifier.jsp),¿É·Ç³£·½±ãµØÈ·¶¨Ä³Ìõrrna»ùÒòÐòÁдÓÃŵ½Êô/ÖÖˮƽµÄ·ÖÀàÐÅÏ¢²¢¸ø³ö¸÷ˮƽÏàÓ¦µÄÖÃÐŶȡ£
4.greengenes (http://greengenes.lbl.gov/) greengenesÊÇרÃÅÕë¶Ôϸ¾ú¡¢¹Å¾ú16s rrna»ùÒòµÄÊý¾Ý¿â,Ïà±ÈÇ°ÃæÌáµ½µÄrdpºÍsilvaÊý¾Ý¿â,¸ÃÊý¾Ý¿â¸üÐÂËٶȽÏÂý,Ä¿Ç°¸üÐÂÍ£ÁôÔÚ2013Äê5Ô¸üеÄgg_13_5°æ±¾(¿ÉÔÚ¸ÃÍøÖ·ÏÂÔØ:http://greengenes.secondgenome.com/downloads/database/13_5),Ä¿Ç°½Ï³£ÓÃÓÚ16s rrna»ùÒò¸ßͨÁ¿²âÐòºó½øÐÐǶºÏÌåÈ¥³ýµÄ²Î±ÈÊý¾Ý¿â¡£Ä¿Ç°,±È½Ï»ðµÄÒ»¸ö·ÖÎö¡ª¡ªpicrust,¼´¸ù¾Ý16s rrna¸ßͨÁ¿²âÐò½á¹ûÔ¤²â΢ÉúÎïȺÂ书ÄܵķÖÎö,Ò²ÊÇ»ùÓÚgg_13_5Êý¾Ý¿â¿ª·¢µÄ,Òò´Ë,Ïë×öpicrust·ÖÎöÒ²±ØÐëÒÀÍÐgreengenesµÄgg_13_5Êý¾Ý¿â½øÐбȶԡ£
5.ezbiocloud ( http://www.ezbiocloud.net/dashboard)ezbiocloudÊÇÓëgreengenesÊý¾Ý¿âÀàËÆ,Ò²ÊÇרÃÅÕë¶Ôϸ¾ú¡¢¹Å¾ú16srrna»ùÒòµÄÊý¾Ý¿â,µ«ÆäÌصãÊÇÒÔ¿ÉÅàÑøµÄϸ¾ú¡¢¹Å¾ú16s rrna»ùÒòÐòÁÐΪÖ÷¡£¸ÃÊý¾Ý¿â¶ÔÓë2016Äê10ÔÂ1ÈÕ½øÐÐÁËÍøÕ¾¸üÐÂ,ÆäÖÐ×î³£ÓõŦÄÜÊÇͨ¹ýÓë¸ÃÊý¾Ý¿â±È¶Ô,È·¶¨Ä³16s rrna»ùÒòÐòÁжÔÓ¦ÎïÖÖÔÚÊý¾Ý¿âÖеĽüÔµ¿ÉÅàÑø/ģʽÖÖ,´ËʱÓõ½µÄÊÇÊý¾Ý¿âµÄidentify¹¦ÄÜ(http://www.ezbiocloud.net/identify),ÍøÕ¾ÒªÇóÓ¦Óøù¦ÄÜʱÐèÒªÏÈͨ¹ýÓÊÏä×¢²áºó·½¿ÉʹÓá£Ïà±ÈÉÏÃæÌáµ½µÄrdp¡¢silvaºÍgreengenesÀ´Ëµ,¸ÃÊý¾Ý¿â½ÏÉÙÓÃÓÚ16s¸ßͨÁ¿²âÐòºóµÄ²Î±ÈÊý¾Ý¿â¡£
6.phytoref(http://phytoref.sb-roscoff.fr/)phytorefÊý¾Ý¿âÊÇרÃÅÕë¶ÔÖÊÌå(plastid)ÖÐ16srrna»ùÒòµÄÊý¾Ý¿â¡£ËùÓнµØ¡¢µË®¡¢º£ÑóÖеĺ¬ÖÊÌåÉúÎï16s rrna»ùÒòÐòÁж¼ÄÒÀ¨ÔÚ¸ÃÊý¾Ý¿âÄÚ,°üÀ¨Â½µØÖ²Îï¡¢º£ÑóºÍµË®´óÐͺÍ΢ÐÍÔåÀàµÈµÄÖÊÌå¡£
7.pfr2(http://pfr2.sb-roscoff.fr/)¸¡ÓÎÓп׳æ½ç(planktonic foraminifera /rhizaria)ÊÇÒ»ÀàÔÚº£ÑóÖй㷺´æÔڵĸ¡ÓÎÔÉúÉúÎï,ÆäÔÚº£Ñó̼ѻ·ÖÐÆðÖØÒª×÷ÓÃ,ÇÒÆ仯ʯ¿ÉÓÃÒÔÉúÎïÄê´úµØ²ãºÍ¹ÅÆøºòÖؽ¨¡£pfr2ÊÇרÃÅÕë¶Ô¸¡ÓÎÓп׳æ½ç18srrna»ùÒòµÄÊý¾Ý¿â¡£Ä¿Ç°¸üа汾Ϊ1.0,ÓÚ2015Äê1ÔÂ20ÈÕÊÍ·Å,°üº¬3322Ìõ¸ßÖÊÁ¿µÄ¸¡ÓÎÓп׳æ½ç18s rrna»ùÒòÐòÁС£
Îå¡¢sirnaÊý¾Ý¿â¼°Éè¼Æ¹¤¾ß
1.sirna databasesearchable database of silencer ™ validated and pre-designed sirnas to >34,000 human, mouse, and rat targets. all sirnas in the database have been designed for maximum potency and specificity using a well-tested, proprietary algorithm . and silencing results are guaranteed.
2.sirna target finder find sirna target sites in your mrna of interest using the published recommendations of tuschl and colleagues for sirna design. once identified, sirna targets can be sent directly to one of the kit-specific design tools described below or subjected to a blast search by clicking on the appropriate link below the target of interest.
3.silencer™ sirna construction kit template design tool once the target sequence of your sirna has been chosen, use this tool to determine the sequences of the sense and antisense sirna oligonucleotide templates. the program adds "cctgtctc" (complementary to the t7 promoter primer supplied in the kit) to the 3' end of each oligonucleotide.
4.psilencer™ expression vectors insert design tool this tool generates hairpin sirna-encoding dna oligonucleotide inserts from an input sirna target sequence. the program will add the loop sequence and overhangs for cloning as outlined in the vectors' instruction manuals.
5.silencer™ express sirna expression cassette kits pcr primer design tool this tool generates template dna oligonucleotide sequences from an input sirna target sequence. designs for both the "two-oligonucleotide" and "single-oligonucleotide" approach are displayed. these designs are generated using the loop, terminator and rna polymerase promoter sequences described in the kits' instruction manual.
6¡¢protein lounge :http://www.proteinlounge.com/
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