for example:

cd /fml/ag-raetsch/share/projects/genefinding/C_elegans/nGASP_alignments
cd /fml/ag-raetsch/share/projects/genomes/Caenorhabditis_elegans_WS180
cd /fml/ag-raetsch/share/projects/genomes/Caenorhabditis_briggsae
cd /fml/ag-raetsch/share/projects/genomes/Caenorhabditis_remanei
cd /fml/ag-raetsch/share/projects/genomes/Caenorhabditis_PB2801 

then:

start matlab

addpath ~/svn/tools/genomes/
genome_info = init_genome('genome.config')

addpath ~/svn/projects/splicing/splicegraphs/detect_altsplice/
addpath ~/svn/projects/splicing/splicegraphs/     

cd ~/svn/projects/splicing/gff/read_sequences/
read_confirmed_sequences

addpath ~/svn/projects/genefinding/data_processing_lsl/signal_masks/
gen_signal_masks(genome_info)

