any good R package to scan microRNA target?
1
0
Entering edit mode
wang peter ★ 2.0k
@wang-peter-4647
Last seen 8.1 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 • 966 views
ADD COMMENT
0
Entering edit mode
@steve-lianoglou-2771
Last seen 4 weeks 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
0
Entering edit mode
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
0
Entering edit mode
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
0
Entering edit mode
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
0
Entering edit mode
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
0
Entering edit mode
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

Login before adding your answer.

Traffic: 442 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6