Schema for D. mel Proteins - Spaln Alignment of D. melanogaster Proteins
  Database: DereCAF1    Primary Table: spalnDm3Proteins    Row Count: 30,019   Data last updated: 2024-08-24
fieldexampleSQL type info
bin 585smallint(5) unsigned range
chrom scaffold_1390varchar(255) values
chromStart 1230int(10) unsigned range
chromEnd 3836int(10) unsigned range
name mt:ND1-PBvarchar(255) values
score 1199int(10) unsigned range
strand +char(1) values
thickStart 1230int(10) unsigned range
thickEnd 3836int(10) unsigned range
reserved 0int(10) unsigned range
blockCount 2int(10) unsigned range
blockSizes 4,935,longblob  
chromStarts 0,1671longblob  

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStarts
585scaffold_139012303836mt:ND1-PB1199+12303836024,935,0,1671
585scaffold_139039545067mt:Cyt-b-PB1409-39545067011113,0
585scaffold_139050735985mt:ND6-PA697-5073598502530,4,0,908
585scaffold_139057306018mt:ND4L-PA439+5730601801288,0
585scaffold_139060207352mt:ND4-PB1378+60207352011332,0
585scaffold_139074409123mt:ND5-PB1761+74409123011683,0
585scaffold_1390964911924mt:ND3-PA412-96491192402324,3,0,2272
585scaffold_13901007410848mt:CoIII-PA710-100741084801774,0
585scaffold_13901085011522mt:ATPase6-PB806-108501152201672,0
585scaffold_13901183812501mt:CoII-PA850-118381250101663,0

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

D. mel Proteins (spalnDm3Proteins) Track Description
 

Description

D. melanogaster proteins annotated by FlyBase were aligned against the D. erecta genome assembly using Spaln2 with cross-species parameters.

Methods

D. melanogaster proteins were mapped against the D. erecta 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