Question

any good R package to scan microRNA target?

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wang peter ★ 2.0k

@wang-peter-4647

Last seen 9.8 years ago

i have microRNA sequences and 3'UTR sequences i donot know which R package to scan microRNA target? thank you if you have coding,please share with me -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839 at cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253

microRNA microRNA • 1.4k views

ADD COMMENT • link updated 12.3 years ago by Steve Lianoglou ★ 13k • written 12.3 years ago by wang peter ★ 2.0k

score 0 · Answer 1 · 2012-03-16

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Steve Lianoglou ★ 13k

@steve-lianoglou-2771

Last seen 16 months ago

United States

Hi, On Fri, Mar 16, 2012 at 3:00 PM, wang peter <wng.peter at="" gmail.com=""> wrote: > i have microRNA sequences and 3'UTR sequences > i donot know which R package to scan microRNA target? Does the string matching functionality provided in Biostrings not get you where you want to be? cf. matchPattern and friends. Of course, miRNA seed matches don't tell the whole (?any?)) of the story, so ... are you looking for something more "sophisticated," or? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

ADD COMMENT • link 12.3 years ago Steve Lianoglou ★ 13k

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no, it is not so simple there are many algorithms to scan microRNA on 3'UTR NOT match? SOME people call it miRNA target prediction like picTar or miRanda -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839 at cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253

ADD REPLY • link 12.3 years ago wang peter ★ 2.0k

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On Fri, Mar 16, 2012 at 3:15 PM, wang peter <wng.peter at="" gmail.com=""> wrote: > no, > it is not so simple > there are many algorithms to scan microRNA on 3'UTR > NOT match? > SOME people call it miRNA target prediction > like picTar or miRanda It's true -- and SOME people don't really put too much faith in such predictions, is what I'm saying (that's where my "some (?any?) of story" comment came from ;-) But anyway -- so you're looking for an R wrapper to picTar, or miRanda, or targetscan, or mirSVR, or? -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

ADD REPLY • link 12.3 years ago Steve Lianoglou ★ 13k

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Also: On Fri, Mar 16, 2012 at 3:18 PM, Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> wrote: > On Fri, Mar 16, 2012 at 3:15 PM, wang peter <wng.peter at="" gmail.com=""> wrote: >> no, >> it is not so simple >> there are many algorithms to scan microRNA on 3'UTR >> NOT match? >> SOME people call it miRNA target prediction >> like picTar or miRanda > > It's true -- and SOME people don't really put too much faith in such > predictions, is what I'm saying (that's where my "some (?any?) of > story" comment came from ;-) > > But anyway -- so you're looking for an R wrapper to picTar, or > miRanda, or targetscan, or mirSVR, or? I bet you'd get pretty close to such methods by doing a seed match (w/ or w/o m1A rule) and filter by conservation if you want to do some type of analysis (functional enrichments of "targets", or something). If you want to do better, see if you can't encourage your collaborators to do some type of differential *-CLIP experiment ... more data == more fun :-) -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

ADD REPLY • link 12.3 years ago Steve Lianoglou ★ 13k

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yeah you are totally right i need a pipeline also, we developed a miRNA target prediction software-- humitar but i need a pipeline -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839 at cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253

ADD REPLY • link 12.3 years ago wang peter ★ 2.0k

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Hi, On Fri, Mar 16, 2012 at 3:27 PM, wang peter <wng.peter at="" gmail.com=""> wrote: > yeah > you are totally right > i need a pipeline > > also, we developed a miRNA target prediction software-- humitar > but i need a pipeline Seems like you're perfectly positioned to whip up a humitaR package, then ;-) -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

ADD REPLY • link 12.3 years ago Steve Lianoglou ★ 13k