What's Your Problem? Open Thread
Welcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours.
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Comments
Comment from Mary
Time February 18, 2008 at 8:13 AM
Glad you like WYP–and we know it takes time to build some community around it, we aren’t worried (yet!). It is new.
Some other microRNA features I know:
The TargetScan features are applied as a track to the UCSC Genome Browser: http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=103888287&c=chrX&g=targetScanS
http://miRNAMap.mbc.nctu.edu.tw/ miRNAMap 2.0
http://genome.ewha.ac.kr/miRGator/miRGator.html miRGator
http://alk.ibms.sinica.edu.tw/ For viruses: Vir-Mir
http://www.bioinformatics.org/mirfinder/ miRFinder
http://wotan.wistar.upenn.edu/NBmiRTar/login.php NBmiRTar
http://bioinfo.au.tsinghua.edu.cn/miralign/ MiRAlign
Some of them seem to be pipelines that include some of the other tools–but maybe the interfaces will be preferable or the additional features may help.
Anyone who knows of other tools should let us know–we love to hear about new tools.
http://www.rnaiweb.com/RNAi/MicroRNA/MicroRNA_Tools___Software/MicroRNA_Target_Scan/index.html
Comment from Mary
Time February 18, 2008 at 8:47 AM
Ok, had more coffee, dug up some others:
http://compbio.utmem.edu/miRSNP/ SNPs in miRNA target sites.
http://cbit.snu.ac.kr/~ProMiR2/ ProMir II
http://bioinfo3.noble.org/miRNA/miRU.htm Plant focused
http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/ RNAhybrid
http://www-ab.informatik.uni-tuebingen.de/software/crosslink/welcome.html CrossLink
Comment from bill
Time February 18, 2008 at 1:27 PM
Thank you so much! It’ll take me a month to find enough “mess around on the web” time to go through all those.
Comment from Mary
Time February 18, 2008 at 1:38 PM
Welcome!
If you find some you prefer for specific reasons of your research, come back and tell us about them. Some will be more or less suited to a given project.
Comment from bill
Time February 18, 2008 at 4:59 AM
This is very broad, so feel free to not do my damn homework for me — but I love the idea of a WYP feature and you don’t have any takers yet, so: what resources are available for researching (and predicting) the involvement of microRNA in the regulation of a particular protein? I know about miRBase and TargetScan, but would love to hear about others.