Schema for Potential Frame Shifts - Potential Frame Shifts Detected by SPALN2
  Database: DbipGB2    Primary Table: spalnDm3FrameShift    Row Count: 1,189   Data last updated: 2024-01-05
fieldexampleSQL type info
chrom AFFE02000413varchar(255) values
chromStart 2832int(10) unsigned range
chromEnd 2833int(10) unsigned range
name Cdk8-PA_frameshiftvarchar(255) values
id Cdk8-PAvarchar(255) values
description FrameShift=-1longblob  

Sample Rows
 
chromchromStartchromEndnameiddescription
AFFE0200041328322833Cdk8-PA_frameshiftCdk8-PAFrameShift=-1
AFFE0200071388438844CG32847-PB_frameshiftCG32847-PBFrameShift=-1
AFFE020023266970mt:Cyt-b-PB_frameshiftmt:Cyt-b-PBFrameShift=1
AFFE02002326518519mt:ND1-PB_frameshiftmt:ND1-PBFrameShift=2
AFFE02002326537538mt:ND1-PB_frameshiftmt:ND1-PBFrameShift=1
AFFE02002326705706mt:ND1-PB_frameshiftmt:ND1-PBFrameShift=1
AFFE02002326743744mt:ND1-PB_frameshiftmt:ND1-PBFrameShift=-1
AFFE02002326793794mt:ND1-PB_frameshiftmt:ND1-PBFrameShift=-1
AFFE02002326900901mt:ND1-PB_frameshiftmt:ND1-PBFrameShift=2
AFFE02002326959960mt:ND1-PB_frameshiftmt:ND1-PBFrameShift=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. bipectinata genome assembly with cross-species parameters.

Methods

D. melanogaster proteins were mapped against the D. bipectinata 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