Index of /species/data/dros-synteny-data

 Name                    Last modified       Size  Description

 Parent Directory        19-Jun-2008 13:51      -  
 dspp-align-gff2tab.sh   10-Nov-2007 14:52     1k  
 dspp_align                                     -  
 dsppsynteny3.R          28-Feb-2006 10:36    15k  
 gff/                    10-Nov-2007 15:13      -  
 muller-elements-output/ 10-Nov-2007 15:31      -  
 tabs-dmel/              10-Nov-2007 14:31      -  
 tabs-dmoj/              10-Nov-2007 14:32      -  
 topscaffolds/           10-Nov-2007 15:26      -  

DATA for http://insects.eugenes.org/species/maps/muller-elements/

These maps show large scale synteny between genome assembly units (scaffolds or chromosomes), 
of 12 Drosophila species, as determined from genome x genome DNA BLAST matches, 
identified as common Muller elements A thru E (small F/Dmel-chr4 is not listed).

Each chromosome picture has the query genome on the left as a "ladder" from 
bottom base 1 to top end, and the synteny source on the right as an arrow. Between are 
colored lines of high matching regions (colors distinguish clusterings). 
Weaker syntenic relations are not shown. Lack of display doesn't mean lack of synteny.

ANALYSIS STEPS:
1. genome x genome blastn alignment to algn summary GFF
   using two source databases: dmel, dmoj chromosomes

set source=dmoj
foreach dp ($drosophila)

 gtar -Ozxf $soc/${dp3}${source}.bloutiu.tgz |\
   blast92gff.pl -noswap -in=stdin -gff -deshredquery -add_match -uniq -nodebug \
    -chrin=$scaffoldgff  -qdb=${dpid} -out=$source-${dp3}-dna.gff 

 chrgff2align.pl -stats -in=$source-${dp3}-dna.gff -out=$source-${dp3}-algn.gff \
   > & $source-${dp3}-algn.stats 

Result algn.gff in dspp_align/

2.  Convert algn GFF to R table, see dspp-align-gff2tab.sh
   
Result in tabs-$source/

3.  R statistics clustering genome x genome alignments to show major syntenic regions
    using dist, hclust. See dsppsynteny3.R

Output chromosome synteny plots, HTML files.  Result in muller-elements-output/

Author: Don Gilbert, Analysis date: Feb. 2006