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Table 8 Parameters used with BLASTZ and StemPrediction.

From: A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins

 

Parameter

Value

Description

BLASTZ

O

150

Gap

 

E

100

Gap

 

K

500

Maximal segment pair (MSP) score

 

L

500

Gapped alignment threshold

 

W

6

Word size

StemPrediction

   
 

MIN_ARM_LENGTH

16

Minimum stem arm length (nt)

 

MAX_ENERGY

-15.0

Minimum free energy of the stem

 

MAX_BULGE_SIZE

5

Maximum number of unpaired nt on a single strand in the stem

 

MAX_BULGE_BASES

7

Maximum number of unpaired nt on both strand in the stem

 

MAX_GLUE_DISTANCE

10

Maximum distance for two stems to be glued (joined) StemPrediction

 

MAX_FILTER_ENERGY

-15.0

Minimum free energy of the glued stem