Schema for Potential Frame Shifts - Potential Frame Shifts Detected by SPALN2

Database: DsuzGB1 Primary Table: spalnDm3FrameShift Row Count: 4,015 Data last updated: 2024-01-05

field	example	SQL type	info
`chrom`	AWUT01014734	`varchar(255)`	values
`chromStart`	16344	`int(10) unsigned`	range
`chromEnd`	16345	`int(10) unsigned`	range
`name`	CG42784-PC_frameshift	`varchar(255)`	values
`id`	CG42784-PC	`varchar(255)`	values
`description`	FrameShift=-1	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	id	description
AWUT01014734	16344	16345	CG42784-PC_frameshift	CG42784-PC	FrameShift=-1
AWUT01015449	21888	21889	pAbp-PA_frameshift	pAbp-PA	FrameShift=2
AWUT01015449	21888	21889	pAbp-PB_frameshift	pAbp-PB	FrameShift=2
AWUT01015449	21888	21889	pAbp-PC_frameshift	pAbp-PC	FrameShift=2
AWUT01016850	5106	5107	DIP1-PF_frameshift	DIP1-PF	FrameShift=1
AWUT01016850	5106	5107	DIP1-PB_frameshift	DIP1-PB	FrameShift=1
AWUT01017137	1190	1191	ssp5-PA_frameshift	ssp5-PA	FrameShift=-2
AWUT01017252	3439	3440	Cyfip-PA_frameshift	Cyfip-PA	FrameShift=-1
AWUT01017432	3254	3255	ens-PC_frameshift	ens-PC	FrameShift=-2
AWUT01017612	2831	2832	Mrp5-PD_frameshift	Mrp5-PD	FrameShift=-1

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

Potential Frame Shifts (spalnDm3FrameShift) Track Description


	Description Potential frame-shifts identified by Spaln2 when aligning D. melanogaster proteins against the D. suzukii genome assembly with cross-species parameters. Methods D. melanogaster proteins were mapped against the D. suzukii genome assembly with tblastn. For each protein, the region surrounding the best tblastn hit is identified and each protein is re-aligned against this genomic region with Spaln2 using cross-species parameters optimized for D. melanogaster: (-Tdromel -yX). References Iwata H., and Gotoh, O. Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features. Nucleic Acids Research. 2012, 109

Description