Question

Algal microRNA prediction

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10.3 years ago

lakshmi.bioinformatics ▴ 30

Is there a possibility to predict algal microRNA using the transcriptome data of the algae alone

If yes, kindly quote the reference if possible

Thanks in advance

RNA-Seq • 2.0k views

ADD COMMENT • link updated 2.9 years ago by Ram 44k • written 10.3 years ago by lakshmi.bioinformatics ▴ 30

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you can use mirdeep to predict miRNAs, but the main problem is that you don't have small RNA data. The protocol is total different and mainly you lose small fragments, and if the rnaseq has been enriched to get poly-A genes, for sure you won't have anything.

ADD REPLY • link 10.1 years ago by Lorena Pantano ▴ 380

score 2 · Answer 1 · 2014-10-06

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10.1 years ago

Renesh ★ 2.2k

I think this is not good idea to predict miRNA from transcriptome data. Transcriptome represents the coding sequences, whereas miRNA are non-coding sequences. Therefore, biological your transcriptome should not contain miRNA.

If you want to confer this you can align your transcriptome data to RFAM and miRNAse database. If there is any non-coding sequences represented in your transcriptome you can find it by looking at aligned data.