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

Database: DsimGB2 Primary Table: spalnDm3FrameShift Row Count: 1,765 Data last updated: 2024-01-05

field	example	SQL type	info
`chrom`	CM002910	`varchar(255)`	values
`chromStart`	212549	`int(10) unsigned`	range
`chromEnd`	212550	`int(10) unsigned`	range
`name`	kis-PA_frameshift	`varchar(255)`	values
`id`	kis-PA	`varchar(255)`	values
`description`	FrameShift=1	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	id	description
CM002910	212549	212550	kis-PA_frameshift	kis-PA	FrameShift=1
CM002910	212549	212550	kis-PE_frameshift	kis-PE	FrameShift=1
CM002910	212549	212550	kis-PD_frameshift	kis-PD	FrameShift=1
CM002910	212549	212550	kis-PC_frameshift	kis-PC	FrameShift=1
CM002910	312320	312321	CG43755-PD_frameshift	CG43755-PD	FrameShift=-1
CM002910	561412	561413	Gsc-PE_frameshift	Gsc-PE	FrameShift=1
CM002910	836420	836421	PNUTS-PA_frameshift	PNUTS-PA	FrameShift=-1
CM002910	836420	836421	PNUTS-PB_frameshift	PNUTS-PB	FrameShift=-1
CM002910	1226879	1226880	robo3-PA_frameshift	robo3-PA	FrameShift=-1
CM002910	1226879	1226880	robo3-PC_frameshift	robo3-PC	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. simulans genome assembly with cross-species parameters. Methods D. melanogaster proteins were mapped against the D. simulans 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