Long non coding RNA annotation

[geneart]

Rfam blastn search

Hello all,
I am trying to analyze miRNA data and am at a point to clear off all "junk" sequences from my data. In order to do that I used Rfam fasta files, locally installed as a database but performed a blastn (locally installed) to see what matches I get. Well.....there was no result output whatsoever. My blastn parameters were W7 and e-value of 1000.
Does anyone have experience using Rfam locally and instead of performing a CM SCAN that Rfam recommends ,performed a blastn?
or any thought on this also helps
Thanks in advance.
geneart.

[Aish]

Dear Parthav,
Could you please explain in detail on how to use lncRscan for mining lncRNAs from RNA Seq data?
I am not able to download the lncRscan program.

[ParthavJailwala]

If you start with cufflinks pipeline output for annotation of long ncRNA, then lncRscan is one tool that can be used. It essentially uses the 'class_code' flags in the cuffmerge output file (merged.gtf) to identify potential ncRNA.

We recently used it on a mouse RNA-seq dataset, but are yet to validate the predicted lncRNA from this pipeline.

I will love to hear from others on what tools/strategies are employed to mine an RNA-seq transcriptome to identify & annotate short and long ncRNA.

Thanks
Parthav

Hi, how you identified the lncRNA and what was your refseq

[samsonn]

Hi, how you identified the lncRNA and what was your refseq

[ppgardne]

Google is your friend:

http://rfam.sanger.ac.uk/

http://www.ensembl.org/index.html

http://www.ensembl.org/biomart/martview

[Giorgio C]

Thank you for your answer.
Can you send me the link for both the database? Thanks

[ppgardne]

Havanna curates annotation of long ncRNAs (they call them "processed transcripts"). Rfam annotates short ncRNAs. All annotation for human is available from ENSEMBL and the BioMart.

[Giorgio C]

Hy,
I have a transcriptome dataset assembled and partially annotated. I have more than 1000 non coding Sequences that didnt' mach with Blast (transctipome-hg19). Could you say me any tool, database to classify this sequences or to determinate the % of miRNA, snoRNA. etc. ?
(mirTool give me strange results with 100% unclassified, impossible)
Have you any idea?
Thank you very much