Index of /species/data/work/motifs

 Name                    Last modified       Size  Description

 Parent Directory        03-Apr-2008 14:55      -  
 cdsgff2seq.pl           02-Mar-2007 18:02    19k  
 data/                   02-Mar-2007 17:00      -  
 logo-pictures/          02-Mar-2007 16:36      -  
 nmica/                  02-Mar-2007 16:51      -  

Sample motifs around gene or exon boundaries.

Logo pictures are drawn with   http://bespoke.lbl.gov/weblogo/
See also http://www.sanger.ac.uk/Software/analysis/nmica/
for analyzing gene subset sequences for motifs.

The program cdsgff2seq.pl is used from pulling subset seq. from GFF data (exons,CDS/genes)
See there for further information. 

## extract region.gff
## extract region up/down/in motif seq
cdsgff2seq.pl -a genestart -o -90,9 -t exon region.gff chromfa.dir/ > gene-begin.fa
cdsgff2seq.pl -a geneend -o -9,90 -t exon region.gff chromfa.dir/ > gene-end.fa
cdsgff2seq.pl -a intronstart -o -19,20 -t exon region.gff chromfa.dir/ > intron-begin.fa
cdsgff2seq.pl -a intronend -o -19,20 -t exon region.gff chromfa.dir/ > intron-end.fa

Sample Drosophila Est-6 six-pack regions:
dmoj/scaffold_6540:24423577..24448576
dvir/scaffold_12855:9338335..9363334
dpse/XR_group6:2503342..2528341
dper/scaffold_9:798097..823096
dwil/scaffold_180949:5111643..5121642
dgri/scaffold_14830:1806937..1816936
dana/scaffold_13337:1444999..1469998