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

Database: DyakCAF1 Primary Table: spalnDm3FrameShift Row Count: 1,823 Data last updated: 2024-01-05

field	example	SQL type	info
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	26791	`int(10) unsigned`	range
`chromEnd`	26792	`int(10) unsigned`	range
`name`	Cda5-PB_frameshift	`varchar(255)`	values
`id`	Cda5-PB	`varchar(255)`	values
`description`	FrameShift=-1	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	id	description
chr2L	26791	26792	Cda5-PB_frameshift	Cda5-PB	FrameShift=-1
chr2L	26961	26962	Cda5-PB_frameshift	Cda5-PB	FrameShift=-1
chr2L	26980	26981	Cda5-PB_frameshift	Cda5-PB	FrameShift=-2
chr2L	27080	27081	Cda5-PB_frameshift	Cda5-PB	FrameShift=-2
chr2L	27366	27367	Cda5-PB_frameshift	Cda5-PB	FrameShift=1
chr2L	29810	29811	Cda5-PG_frameshift	Cda5-PG	FrameShift=1
chr2L	29810	29811	Cda5-PF_frameshift	Cda5-PF	FrameShift=1
chr2L	29810	29811	Cda5-PJ_frameshift	Cda5-PJ	FrameShift=1
chr2L	186929	186930	spen-PC_frameshift	spen-PC	FrameShift=-2
chr2L	186929	186930	spen-PA_frameshift	spen-PA	FrameShift=-2

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. yakuba genome assembly with cross-species parameters. Methods D. melanogaster proteins were mapped against the D. yakuba 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