Table 4

Criteria for visual inspection of intergenic regions in Streptococcus pyogenes NZ311

start

1) BLAST vs Streptococci

2) BLAST vs S. pyogenes

3) DNA base stacking energy

4) RNAfold


1

202790

X

X


2

216807

X

X

X


3

273446

X

X

X


4

308253

X

X

X


5

349593

X

X

X


6

362796

X

X


7

363720

X

X

X


8

407642

X

X


9

506298

X

X

X


10

512500

X

X

X


11

554314

X

X

X


12

568980

X

X

X


13

806825

X

X


14

827250

X

X


15

949486

X

X


16

1201476

X

X


17

1487751

X

X

X


18

1571435

X

X


19

1581266

X


20

1704825

X

X

X


Criteria: 1) increased conservation shown by BLAST against selected Streptococci genomes (see the moses website for a List). 2) increased conservation shown by BLAST against all Streptococcus pyogenes substrains. 3) increased DNA base stacking energy profile or presence of two nearby peaks. 4) a peak in the RNAfold profile.

Raasch et al. BMC Bioinformatics 2010 11:491   doi:10.1186/1471-2105-11-491

Open Data