Schema for D. mel Non-coding RNAs - FASTA alignment of D. melanoagster Non-coding RNAs

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Schema for D. mel Non-coding RNAs - FASTA alignment of D. melanoagster Non-coding RNAs

Database: DmojImproved Primary Table: dmel_ncRNA Row Count: 1,019

field	example	SQL type	info
`bin`	586	`smallint(5) unsigned`	range
`chrom`	improved_6498	`varchar(255)`	values
`chromStart`	167393	`int(10) unsigned`	range
`chromEnd`	243771	`int(10) unsigned`	range
`name`	FBtr0340011	`varchar(255)`	values
`score`	137	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	167393	`int(10) unsigned`	range
`thickEnd`	243771	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	5	`int(10) unsigned`	range
`blockSizes`	1353,241,1304,151,294,	`longblob`
`chromStarts`	0,45038,57887,70380,76084,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	reserved	blockCount	blockSizes	chromStarts
586	improved_6498	167393	243771	FBtr0340011	137	-	167393	243771	0	5	1353,241,1304,151,294,	0,45038,57887,70380,76084,
592	improved_6498	933075	933215	FBtr0329833	60	-	933075	933215	0	1	140,	0,
603	improved_6498	2472779	2473133	FBtr0309072	97	-	2472779	2473133	0	1	354,	0,
75	improved_6498	2582643	2648234	FBtr0334490	225	-	2582643	2648234	0	5	612,558,484,322,504,	0,48774,49743,50581,65087,
605	improved_6498	2699385	2750284	FBtr0339944	138	-	2699385	2750284	0	5	766,694,742,1244,695,	0,1074,3958,38791,50204,
75	improved_6498	2699414	2794847	FBtr0333704	193	-	2699414	2794847	0	10	830,322,561,163,892,507,552,255,765,121,	0,857,1360,14383,19973,25550,38770,72903,84267,95312,
608	improved_6498	3017057	3063048	FBtr0302350	139	+	3017057	3063048	0	3	783,2511,1855,	0,35052,44136,
608	improved_6498	3017057	3063048	FBtr0335261	129	+	3017057	3063048	0	3	783,2578,1855,	0,34985,44136,
610	improved_6498	3329073	3406424	FBtr0300146	128	+	3329073	3406424	0	20	703,617,498,1072,707,750,735,1073,611,688,664,823,470,689,426,689,819,820,1076,559,	0,24936,30688,57449,58539,59246,60023,60758,61923,64403,65617,66548,67385,67966,68667,69120,70180,71245,75703,76792,
610	improved_6498	3359975	3406485	FBtr0339732	96	-	3359975	3406485	0	14	358,270,410,328,260,270,410,406,301,371,416,384,413,424,	0,26417,27349,27768,29408,29726,30659,36188,39790,40460,40885,44385,45604,46086,

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

D. mel Non-coding RNAs (dmel_ncRNA) Track Description


	Description This track shows the FASTA alignment of D. melanogaster non-coding RNA's against the D. mojavensis assembly. Methods Non-coding RNAs in D. melanogaster were retrieved from FlyBase and mapped against the D. mojavensis assembly using FASTA with the following parameters: -H -b 9999999 -n -q -3 -f 10 -g 10 -m 8 -U -r "+5/-4" -b 1 -E 1e-03 References The D. melanogaster non-coding RNAs are available for download at FlyBase Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 April; 85(8): 2444–2448.