Schema for Potential Frame Shifts - Potential Frame Shifts Detected by SPALN2
  Database: DanaWGS    Primary Table: spalnDm3FrameShift    Row Count: 1,903
fieldexampleSQL type info
chrom scaffold_10103varchar(255) values
chromStart 624int(10) unsigned range
chromEnd 625int(10) unsigned range
name CG16952-PE_frameshiftvarchar(255) values
id FBpp0309048varchar(255) values
description Frameshift=2longblob  

Sample Rows
 
chromchromStartchromEndnameiddescription
scaffold_10103624625CG16952-PE_frameshiftFBpp0309048Frameshift=2
scaffold_1010310551056CG16952-PB_frameshiftFBpp0073925Frameshift=-1
scaffold_1010310551056CG16952-PA_frameshiftFBpp0073924Frameshift=-1
scaffold_1010310551056CG16952-PC_frameshiftFBpp0073926Frameshift=-1
scaffold_1010310551056CG16952-PD_frameshiftFBpp0290025Frameshift=-1
scaffold_1010310551056CG16952-PE_frameshiftFBpp0309048Frameshift=-1
scaffold_1010318011802CG16952-PA_frameshiftFBpp0073924Frameshift=-1
scaffold_1010318011802CG16952-PB_frameshiftFBpp0073925Frameshift=-1
scaffold_1010318011802CG16952-PC_frameshiftFBpp0073926Frameshift=-1
scaffold_1010318011802CG16952-PD_frameshiftFBpp0290025Frameshift=-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. ananassae genome assembly with cross-species parameters.

Methods

D. melanogaster proteins were mapped against the D. ananassae 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