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Old 02-15-2014, 08:28 AM   #1
raghavagps
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Location: Chandigarh, India

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Smile Classification of non-coding RNA

May I know your feedback on our recently developed web server RNAcon, which allows prediction and classification of non-coding RNAs. It uses SVM-based model for the discrimination between coding and ncRNAs and RandomForest-based prediction model for the classification of ncRNAs into different classes. The structural information based graph properties were used for the development of prediction model. Feedback of researchers/users is very important for developing better methods.

See http://www.biomedcentral.com/1471-2164/15/127

http://crdd.osdd.net/raghava/rnacon/
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# Institute of Microbial Technology, Sector-39A, Chandigarh, India #
# Phone: +91-172-2690557, Fax: +91-172-2690632 #
# Eadd: http://www.imtech.res.in/raghava/ raghava@imtech.res.in #
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Old 02-15-2014, 03:04 PM   #2
dietmar13
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Location: Vienna

Join Date: Mar 2010
Posts: 107
Default new biostrings R-package ...

the new "biostrings" R-package needs some modifications of the R-script in the progs folder (attached).

and all sequences have to be RNA sequences (uU instead of tT).

using a large file of transcripts, only the first 316 get classified (which type) but all predicted (coding/non-coding).

i get this exception many times:


Code:
Exception in thread "main" java.lang.SecurityException: cannot verify signature block file META-INF/YANNPONT
	at sun.security.util.SignatureFileVerifier.processImpl(SignatureFileVerifier.java:220)
	at sun.security.util.SignatureFileVerifier.process(SignatureFileVerifier.java:193)
	at java.util.jar.JarVerifier.processEntry(JarVerifier.java:307)
	at java.util.jar.JarVerifier.update(JarVerifier.java:218)
	at java.util.jar.JarFile.initializeVerifier(JarFile.java:345)
	at java.util.jar.JarFile.getInputStream(JarFile.java:412)
	at sun.misc.URLClassPath$JarLoader$2.getInputStream(URLClassPath.java:775)
	at sun.misc.Resource.cachedInputStream(Resource.java:77)
	at sun.misc.Resource.getByteBuffer(Resource.java:160)
	at java.net.URLClassLoader.defineClass(URLClassLoader.java:436)
	at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
	at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)
Attached Files
File Type: gz IPKnotGraph2-BPSEQ.R.gz (1.9 KB, 15 views)

Last edited by dietmar13; 02-16-2014 at 01:22 AM.
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Old 02-19-2014, 12:46 AM   #3
Dr. Bharat Panwar
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Location: INDIA

Join Date: Feb 2014
Posts: 1
Default

Dear dietmar13,
Thanks for the comment. The versions that have been used in RNAcon are as follows:

igraph: 0.6.3
Biostrings: 2.24.1
built under R 2.15.1

As most of the users (we enquired) were using the older versions and also as readFASTA() is a more generic method(as compared to readRNAStringSet()), we used the above mentioned versions.

After your kind comment we have rectified the source of the error by conversion of tT to uU in the classifier. We thank you for pointing out the bug. Please reinstall and rerun the RNAcon and let us know if we can assist yourself further...

Thanks and regards...
RNAcon Team
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Old 12-10-2014, 05:26 AM   #4
cganote
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Location: Indiana, US

Join Date: Dec 2012
Posts: 2
Default Trouble installing standalone

Hi Devs,

I'm having the same issue getting Varna to get through the security part. I downloaded and set up the cert through jcontrol, installed a new java, and still no luck. I'm running on CentOS and this is one of the hardest suites I've ever tried to install - please advise.

-Carrie
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