#Create database

# took about a minute on mars
lastdb -cR01 yeastdb S_cerevisiae_all.fsa

#Create alignment
# roughly 5 min. ? maybe less
lastal yeastdb S_cerevisiae_all.fsa > S_cerevisiae_all.maf &

# Create dotplot
# about 10 sec.
last-dotplot S_cerevisiae_all.maf S_cerevisiae_allvsall.png

# just show a self-self comparison for a single chromosome
last-dotplot -1 NC_001142 -2 NC_001142  S_cerevisiae_all.maf S_cerevisiae_NC001142self.png


#################### db for both cerevisiae and arboricola
#real	0m37.648s
#user	0m36.319s
#sys	0m0.361s
time lastdb -cR01 CerArb  S_cerevisiae_all.fsa S_arboricola_all.fsa

#Create alignment
# real	5m34.038s
#user	5m16.908s
#sys	0m0.956s
time lastal CerArb S_cerevisiae_all.fsa S_arboricola_all.fsa > CerArb.maf &

# Create dotplot
# real	0m52.206s
#user	0m45.840s
#sys	0m1.394s

time last-dotplot CerArb.maf CerArb.png