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Old 07-22-2011, 05:11 AM   #1
mic_cim
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Location: aus

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Default miRNA target prediction

Hi, is there any resource out there showing example of pipeline in perl language for miRNA target prediction? thanks
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Old 08-19-2011, 09:14 AM   #2
sridharacharya
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Default perl pipeline for miRNA analysis

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Originally Posted by mic_cim View Post
Hi, is there any resource out there showing example of pipeline in perl language for miRNA target prediction? thanks
Hi,

I too have been searching for such a pipeline. So far, I could find only one resource, by Ryan D. Morin.
The URL is below.
http://www.bcgsc.ca/platform/bioinfo...irna-detection

I tried to use the scripts in the pipeline. It seems to be written for inhouse analysis, and I had to change some lines in the scripts for them to correctly work and fit in the pipeline.

It uses RNAFold package to detect secondary structure and uses SVM (through R) to detect candidate miRNA sequences. It also needs MYSQL, and supporting perl modules to fetch genomics sequences from EBI. Though with all these requirements, it is not very difficult to set up the pipeline.

You have to prepare a gff file of the sequence reads with start and end genomic coordinate positions. Then supply it to the pipeline.

It seems to run very slow, especially with large number of sequencing reads, from NGS. I tried to communicate with the author but still awaiting reply.

Let me know if you try this pipeline, and let me know if you could find any other software. I am especially looking for miRNA analysis of color-space SoLiD data.
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