Schema for Potential Frame Shifts - Potential Frame Shifts Detected by SPALN2
  Database: DgriCAF1    Primary Table: spalnDm3FrameShift    Row Count: 1,335   Data last updated: 2024-01-05
fieldexampleSQL type info
chrom scaffold_10068varchar(255) values
chromStart 1278int(10) unsigned range
chromEnd 1279int(10) unsigned range
name ORY-PD_frameshiftvarchar(255) values
id ORY-PDvarchar(255) values
description FrameShift=1longblob  

Sample Rows
 
chromchromStartchromEndnameiddescription
scaffold_1006812781279ORY-PD_frameshiftORY-PDFrameShift=1
scaffold_1390724792480kl-2-PD_frameshiftkl-2-PDFrameShift=1
scaffold_1390726392640kl-2-PD_frameshiftkl-2-PDFrameShift=-1
scaffold_1395415111512CG15145-PA_frameshiftCG15145-PAFrameShift=1
scaffold_1439022122213Reph-PA_frameshiftReph-PAFrameShift=-1
scaffold_1442268286829Hs3st-A-PB_frameshiftHs3st-A-PBFrameShift=1
scaffold_1442268286829Hs3st-A-PA_frameshiftHs3st-A-PAFrameShift=1
scaffold_145924220642207dati-PB_frameshiftdati-PBFrameShift=2
scaffold_145924220642207dati-PD_frameshiftdati-PDFrameShift=2
scaffold_145924220642207dati-PC_frameshiftdati-PCFrameShift=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. grimshawi genome assembly with cross-species parameters.

Methods

D. melanogaster proteins were mapped against the D. grimshawi 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