Schema for tRNA Genes - Transfer RNA Genes Identified by tRNAscan-SE 2.0

Database: DeugGB2 Primary Table: tRNAscanSE2Details Data last updated: 2019-07-06
Big Bed File: /gbdb/DeugGB2/bbi/DeugGB2.tRNAscanSE2Details.bb
Item Count: 376
Format description: tRNAs identified by tRNAscan-SE 2.0

field	example	description
`chrom`	AFPQ02000301	Reference sequence chromosome or scaffold
`chromStart`	623	Start position in chromosome
`chromEnd`	696	End position in chromosome
`name`	tRNA-Val-CAC-AFPQ02000301-1	Short Name of item
`score`	1000	Score from 0-1000
`strand`	+	+ or -
`thickStart`	623	Start of where display should be thick (start codon)
`thickEnd`	696	End of where display should be thick (stop codon)
`reserved`	0,0,0	Used as itemRgb as of 2004-11-22
`blockCount`	1	Number of blocks
`blockSizes`	73	Comma separated list of block sizes
`chromStarts`	0	Start positions relative to chromStart
`tRNAType`	Val	tRNA type
`antiCodon`	CAC	Anticodon
`trnaScore`	77.3	Infernal Score
`hmmScore`	48.20	Primary structure-only (HMM) score
`str2Score`	29.10	Secondary structure-only score
`isotypeCM`	Val	Isotype covariance model
`isotypeScore`	107.2	Isotype score
`notes`	high confidence set	EukHighConfidenceFilter notes

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	reserved	blockCount	blockSizes	chromStarts	tRNAType	antiCodon	trnaScore	hmmScore	str2Score	isotypeCM	isotypeScore	notes
AFPQ02000301	623	696	tRNA-Val-CAC-AFPQ02000301-1	1000	+	623	696	0,0,0	1	73	0	Val	CAC	77.3	48.20	29.10	Val	107.2	high confidence set
AFPQ02000301	1751	1824	tRNA-Val-CAC-AFPQ02000301-2	1000	+	1751	1824	0,0,0	1	73	0	Val	CAC	77.3	48.20	29.10	Val	107.2	high confidence set

tRNA Genes (tRNAscanSE2Details) Track Description


	Description This track shows the locations of tRNA genes predicted by tRNAscan-SE 2.0. References Chan PP, Lowe TM. tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences. Methods Mol Biol. 2019;1962:1-14.

Description

References