Schema for Potential Frame Shifts - Potential Frame Shifts Detected by SPALN2
  Database: DserGB1    Primary Table: spalnDm3FrameShift    Row Count: 9,768   Data last updated: 2024-01-05
fieldexampleSQL type info
chrom MTTC01000009varchar(255) values
chromStart 91584int(10) unsigned range
chromEnd 91585int(10) unsigned range
name Wnt5-PA_frameshiftvarchar(255) values
id Wnt5-PAvarchar(255) values
description FrameShift=1longblob  

Sample Rows
 
chromchromStartchromEndnameiddescription
MTTC010000099158491585Wnt5-PA_frameshiftWnt5-PAFrameShift=1
MTTC010000099158491585Wnt5-PB_frameshiftWnt5-PBFrameShift=1
MTTC010000127094270943CG44439-PA_frameshiftCG44439-PAFrameShift=2
MTTC010000127100671007CG44439-PA_frameshiftCG44439-PAFrameShift=1
MTTC01000012207175207176boly-PA_frameshiftboly-PAFrameShift=-1
MTTC01000012229690229691pdm3-PF_frameshiftpdm3-PFFrameShift=-1
MTTC01000012229690229691pdm3-PC_frameshiftpdm3-PCFrameShift=-1
MTTC01000012229690229691pdm3-PE_frameshiftpdm3-PEFrameShift=-1
MTTC01000012476389476390CG8642-PB_frameshiftCG8642-PBFrameShift=-1
MTTC01000012476427476428CG8642-PB_frameshiftCG8642-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. serrata genome assembly with cross-species parameters.

Methods

D. melanogaster proteins were mapped against the D. serrata 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