Schema for TransposonPSI - Transposons Fragments Identified by TransposonPSI

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Schema for TransposonPSI - Transposons Fragments Identified by TransposonPSI

Database: dm6 Primary Table: transposon_psi Row Count: 7,559

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	49657	`int(10) unsigned`	range
`chromEnd`	52177	`int(10) unsigned`	range
`name`	TPSI_LINE_0	`varchar(255)`	values
`score`	1381	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	49657	`int(10) unsigned`	range
`thickEnd`	52177	`int(10) unsigned`	range
`itemRgb`	200	`int(10) unsigned`	range
`blockCount`	1	`int(10) unsigned`	range
`blockSizes`	2519	`longblob`
`chromStarts`	0	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb	blockCount	blockSizes	chromStarts
585	chr2L	49657	52177	TPSI_LINE_0	1381	+	49657	52177	0,0,200	1	2519	0
585	chr2L	64304	64703	TPSI_LINE_1	137	+	64304	64703	0,0,200	1	398	0
587	chr2L	348646	351796	TPSI_gypsy_2	1926	-	348646	351796	0,0,128	1	3149	0
589	chr2L	627216	627933	TPSI_TY1_Copia_3	139	+	627216	627933	128,0,0	1	716	0
590	chr2L	687867	694803	TPSI_ltr_Roo_4	8851	-	687867	694803	200,0,0	1	6935	0
590	chr2L	770848	771865	TPSI_mariner_5	988	-	770848	771865	0,128,0	1	1016	0
592	chr2L	978149	983630	TPSI_ltr_Roo_6	2887	+	978149	983630	200,0,0	5	1715,350,2396,911,278	0,1714,2006,4404,5202
592	chr2L	997661	1004597	TPSI_ltr_Roo_7	8855	-	997661	1004597	200,0,0	1	6935	0
593	chr2L	1132864	1133851	TPSI_ltr_Roo_8	723	-	1132864	1133851	200,0,0	1	986	0
594	chr2L	1223754	1226904	TPSI_gypsy_9	1932	+	1223754	1226904	0,0,128	1	3149	0

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

TransposonPSI (transposon_psi) Track Description


	Description The D. melanogaster genome is searched against transposons open reading frames (ORF) profiles using TransposonPSI. The types of transposons in the library include ORFs from gypsy and copia polyproteins, cryptons, helitrons, DNA transposons, and LINE retrotransposons. The best chain per locus is shown in this evidence track. Methods TransposonPSI is an analysis tool to identify protein or nucleic acid sequence homology to proteins encoded by diverse families of transposable elements. PSI-Blast is used with a collection of (retro-)transposon ORF homology profiles to identify statistically significant alignments. This method can be used to identify potential transposon ORFs within a protein set, or to identify regions of transposon homology within a larger genome sequence. References The TransposonPSI application is available for download at SourceForge.