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Table 4 Criteria for visual inspection of intergenic regions in Streptococcus pyogenes NZ311

From: Non-coding RNA detection methods combined to improve usability, reproducibility and precision

 

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

  1. 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.