Schema for fRNAdb::fly smallRNA - fRNAdb::fly small-RNA track

Database: hg19 Primary Table: F_fly_smallRNA Row Count: 4,926

field	example	SQL type	info
`bin`	1717	`smallint(5) unsigned`	range
`matches`	19	`int(10) unsigned`	range
`misMatches`	0	`int(10) unsigned`	range
`repMatches`	0	`int(10) unsigned`	range
`nCount`	0	`int(10) unsigned`	range
`qNumInsert`	0	`int(10) unsigned`	range
`qBaseInsert`	0	`int(10) unsigned`	range
`tNumInsert`	0	`int(10) unsigned`	range
`tBaseInsert`	0	`int(10) unsigned`	range
`strand`	-	`char(2)`	values
`qName`	FR407769	`varchar(255)`	values
`qSize`	19	`int(10) unsigned`	range
`qStart`	0	`int(10) unsigned`	range
`qEnd`	19	`int(10) unsigned`	range
`tName`	chr3	`varchar(255)`	values
`tSize`	198022430	`int(10) unsigned`	range
`tStart`	148443734	`int(10) unsigned`	range
`tEnd`	148443753	`int(10) unsigned`	range
`blockCount`	1	`int(10) unsigned`	range
`blockSizes`	19,	`longblob`
`qStarts`	0,	`longblob`
`tStarts`	148443734,	`longblob`

bin	matches	strand	qName	qSize	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
1717	19	-	FR407769	19	19	chr3	198022430	148443734	148443753	1	19,	0,	148443734,
1385	18	+	FR407841	18	18	chr9	141213431	104904793	104904811	1	18,	0,	104904793,
1830	16	-	FR407847	16	16	chr2	243199373	163296056	163296072	1	16,	0,	163296056,
657	16	-	FR407847	16	16	chr8	146364022	9489178	9489194	1	16,	0,	9489178,
2084	16	+	FR407847	16	16	chr2	243199373	196575067	196575083	1	16,	0,	196575067,
886	16	+	FR407847	16	16	chr7	159138663	39554436	39554452	1	16,	0,	39554436,
1317	16	-	FR407847	16	16	chr15	102531392	96020477	96020493	1	16,	0,	96020477,
728	16	-	FR407847	16	16	chrX	155270560	18856839	18856855	1	16,	0,	18856839,
1770	16	+	FR407847	16	16	chr6	171115067	155360981	155360997	1	16,	0,	155360981,
669	16	-	FR407847	16	16	chr21	48129895	11082959	11082975	1	16,	0,	11082959,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Description

This track shows Drosophila melanogaster small RNAs 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.