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

Database: DbiaGB2 Primary Table: spalnDm3FrameShift Row Count: 1,149 Data last updated: 2024-01-05

field	example	SQL type	info
`chrom`	AFFD02000037	`varchar(255)`	values
`chromStart`	7390	`int(10) unsigned`	range
`chromEnd`	7391	`int(10) unsigned`	range
`name`	mia-PC_frameshift	`varchar(255)`	values
`id`	mia-PC	`varchar(255)`	values
`description`	FrameShift=1	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	id	description
AFFD02000037	7390	7391	mia-PC_frameshift	mia-PC	FrameShift=1
AFFD02000037	7390	7391	mia-PA_frameshift	mia-PA	FrameShift=1
AFFD02000037	7390	7391	mia-PB_frameshift	mia-PB	FrameShift=1
AFFD02000600	4758	4759	mRpS5-PC_frameshift	mRpS5-PC	FrameShift=-1
AFFD02000600	4758	4759	mRpS5-PA_frameshift	mRpS5-PA	FrameShift=-1
AFFD02000600	4898	4899	mRpS5-PC_frameshift	mRpS5-PC	FrameShift=-1
AFFD02000600	4898	4899	mRpS5-PA_frameshift	mRpS5-PA	FrameShift=-1
AFFD02000600	5476	5477	mRpS5-PA_frameshift	mRpS5-PA	FrameShift=-1
AFFD02000600	5476	5477	mRpS5-PC_frameshift	mRpS5-PC	FrameShift=-1
AFFD02001720	209	210	mt:CoIII-PA_frameshift	mt:CoIII-PA	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. biarmipes genome assembly with cross-species parameters. Methods D. melanogaster proteins were mapped against the D. biarmipes 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