fRNAdb::piRNA Track Settings

fRNAdb::piRNA track

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Data last updated: 2011-12-22

Description

This track shows Piwi-associated small RNAs (piRNAs) in the functional RNA database [1] v3.0.

Methods

Short sequences (shorter than 30nt) are aligned to genome by SeqMap [2] with 0 mismatch, no-gap and no-repeat.

Other sequences are aligned to genome by BLAT [3] with identity>=99, coverage>=90 and no-repeat.

References

  [1] Kin T, Yamada K, Terai G, Okida H, Yoshinari Y, Ono Y, Kojima A, Kimura Y, Komori T, Asai K.
      fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences.
      Nucleic Acids Res. 2007 Jan;35(Database issue):D145-8.

  [2] Jiang H, Wong WH
      SeqMap: mapping massive amount of oligonucleotides to the genome.
      Bioinformatics. 2008 Oct 15;24(20):2395-6. Epub 2008 Aug 12.
  [3] Kent WJ.
      BLAT--the BLAST-like alignment tool.
      Genome Res. 2002 Apr;12(4):656-64.