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  • Long non coding RNA annotation

    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

  • #2
    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.

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    • #3
      Thank you for your answer.
      Can you send me the link for both the database? Thanks

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      • #5
        Hi, how you identified the lncRNA and what was your refseq

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        • #6
          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

          Originally posted by samsonn View Post
          Hi, how you identified the lncRNA and what was your refseq

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          • #7
            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.

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            • #8
              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.

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