Schema for RefSeq Drosophila Chain/Net - RefSeq Drosophila Genomes, Chain and Net Alignments
  Database: dm6    Primary Table: chainDserRefSeq1    Row Count: 32,347   Data last updated: 2022-08-20
fieldexampleSQL type info
bin 585smallint(5) unsigned range
score 35471double range
tName chr2Lvarchar(255) values
tSize 23513712int(10) unsigned range
tStart 7580int(10) unsigned range
tEnd 9275int(10) unsigned range
qName NW_018367028varchar(255) values
qSize 4525942int(10) unsigned range
qStrand -char(1) values
qStart 690883int(10) unsigned range
qEnd 693086int(10) unsigned range
id 122055int(10) unsigned range

Sample Rows
 
binscoretNametSizetStarttEndqNameqSizeqStrandqStartqEndid
58535471chr2L2351371275809275NW_0183670284525942-690883693086122055
58521211chr2L2351371287299281NW_0183674655769022+46456384646190201668
58518119chr2L2351371287309275NW_0183662216880660+49969924997543228842
58524621chr2L2351371287339275NW_0183670284525942+23433712343875176237
58512845chr2L2351371287339296NW_0183670284525942+37471803747746301038
7313131511chr2L2351371211210828189NW_0183663861789090+10448150147550
58519959chr2L235137122227622705NW_0183663861789090+122530122885212234
58527905chr2L235137122270523259NW_0183663861789090+122888123441155982
5858747chr2L235137122371123903NW_0183663861789090+123444123636395587
58517271chr2L235137122390324213NW_0183663861789090+123638123948238190

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

RefSeq Drosophila Chain/Net (refseqDrosChainNet) Track Description
 

Description

Genomic scaffolds from each Drosophila species are aligned against the D. melanogaster genome assembly (dm6) using LAST with default parameters. The alignments are then processed using the UCSC whole genome alignment protocol (i.e. chaining and netting).

References

Kiełbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res. 2011 Mar;21(3):487-93. doi: 10.1101/gr.113985.110.

Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. doi: 10.1073/pnas.1932072100.