a problem with oligo2.pl - I think.
The modified version is called oligo3.pl. It
removes all complements, including palindromes
(e.g.,TTTAAA). This is ok in our case, because they don't have
any strand bias anyhow.
new oligo6 and the master.pl program I got the
242 AAGAAA GAAGAA
Ecoli_cft073AE014075 (gamma prot)
EcoliO157BA000007 (gamma prot)
Ecoli_K12U00096 (gamma prot)
Salmonella_typhiAE014613 (gamma prot)
Salmonella_typhimuriumAE006468 (gamma prot)
Shigella_flexneriAE005674 (gamma prot)
vibrio_choleraeAE003852 (gamma prot)
Vibrio_parahaemBA000031 (gamma prot)
vibrio_vulnificusAE016795 (gamma prot)
Shewanella_oneidensisAE014299 (gamma prot)
Xanthomonas_citriAE008923 (gamma prot)
xylella_fastAE009442 (gamma prot)
Buchnera_spBA000003 (gamma prot)
wigglesworthiaBA000021 (gamma prot)
WolbachiaAE017196 (gamma prot)
** Is there a limit to how large one could make the oligos? Why would it be meaningless to calculate the bias for a 30mer?
** Do different organisms have the same or similar oligo strand bias? How quickly does the bias change (with respect to the oligo sequence), when one moves to less related organisms. Possible questions to address: Do archaea have the same bias as bacteria? How about genomes for the same species or the same genus?
** To what extent can the oligo starnd bias be explained by the nucleotide stand bios? Can one calculate how big an oligo bias should be expected from a given single nucleotide bias?