Schema for Potential Frame Shifts - Potential Frame Shifts Detected by SPALN2
  Database: DhydGB1    Primary Table: spalnDm3FrameShift    Row Count: 1,787   Data last updated: 2024-01-05
fieldexampleSQL type info
chrom NWQH01000001varchar(255) values
chromStart 446846int(10) unsigned range
chromEnd 446847int(10) unsigned range
name Vap33-PA_frameshiftvarchar(255) values
id Vap33-PAvarchar(255) values
description FrameShift=2longblob  

Sample Rows
 
chromchromStartchromEndnameiddescription
NWQH01000001446846446847Vap33-PA_frameshiftVap33-PAFrameShift=2
NWQH01000001446846446847Vap33-PE_frameshiftVap33-PEFrameShift=2
NWQH01000001446846446847Vap33-PC_frameshiftVap33-PCFrameShift=2
NWQH01000001446846446847Vap33-PB_frameshiftVap33-PBFrameShift=2
NWQH01000001534834534835CG2930-PA_frameshiftCG2930-PAFrameShift=-1
NWQH01000001534834534835CG2930-PD_frameshiftCG2930-PDFrameShift=-1
NWQH01000001534834534835CG2930-PB_frameshiftCG2930-PBFrameShift=-1
NWQH01000001534834534835CG2930-PF_frameshiftCG2930-PFFrameShift=-1
NWQH01000001534834534835CG2930-PE_frameshiftCG2930-PEFrameShift=-1
NWQH01000001565800565801ec-PA_frameshiftec-PAFrameShift=-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. hydei genome assembly with cross-species parameters.

Methods

D. melanogaster proteins were mapped against the D. hydei 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