Schema for fRNAdb::RNAz - fRNAdb::RNAz track

Database: hg19 Primary Table: F_RNAz_set1_90 Row Count: 36,147

field	example	SQL type	info
`bin`	1009	`smallint(5) unsigned`	range
`matches`	190	`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`	FR059824	`varchar(255)`	values
`qSize`	190	`int(10) unsigned`	range
`qStart`	0	`int(10) unsigned`	range
`qEnd`	190	`int(10) unsigned`	range
`tName`	chr17	`varchar(255)`	values
`tSize`	81195210	`int(10) unsigned`	range
`tStart`	55631668	`int(10) unsigned`	range
`tEnd`	55631858	`int(10) unsigned`	range
`blockCount`	1	`int(10) unsigned`	range
`blockSizes`	190,	`longblob`
`qStarts`	0,	`longblob`
`tStarts`	55631668,	`longblob`

bin	matches	strand	qName	qSize	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
1009	190	+	FR059824	190	190	chr17	81195210	55631668	55631858	1	190,	0,	55631668,
1950	287	+	FR026105	287	287	chr1	249250621	178922247	178922534	1	287,	0,	178922247,
1307	120	+	FR127096	120	120	chr6	171115067	94755463	94755583	1	120,	0,	94755463,
1499	130	+	FR147738	130	130	chr3	198022430	119890565	119890695	1	130,	0,	119890565,
1645	222	+	FR219044	222	222	chr5	180915260	139014326	139014548	1	222,	0,	139014326,
794	54	+	FR191952	54	54	chr11	135006516	27518364	27518418	1	54,	0,	27518364,
1695	234	+	FR357792	234	234	chr1	249250621	145585652	145585886	1	234,	0,	145585652,
772	145	+	FR237460	145	145	chr16	90354753	24583977	24584122	1	145,	0,	24583977,
764	119	+	FR326928	119	119	chr4	191154276	23559947	23560066	1	119,	0,	23559947,
1576	138	+	FR381428	138	138	chr7	159138663	129895773	129895911	1	138,	0,	129895773,

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

Description

This track shows conserved non-coding regions predicted by RNAz [1,2].

This track is prepared to give interoperability with the functional RNA database [3] v3.0.

Methods

Short sequences (shorter than 30nt) are aligned to genome by SeqMap [4] with 0 mismatch, no-gap and no-repeat.

Other sequences are aligned to genome by BLAT [5] with identity>=99, coverage>=90 and no-repeat.

And limit results to predicted positions by RNAz.

References

  [1] Washietl S, Hofacker IL, Lukasser M, Huttenhofer A, Stadler PF.
      Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome.
      Nat Biotechnol. 2005 Nov;23(11):1383-90.

  [2] Washietl S, Hofacker IL, Stadler PF.
      Fast and reliable prediction of noncoding RNAs.
      Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2454-9. Epub 2005 Jan 21.

  [3] 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.

  [4] 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.

  [5] Kent WJ.
      BLAT--the BLAST-like alignment tool.
      Genome Res. 2002 Apr;12(4):656-64.