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Table 1 The blast parameters used to perform the BLAST queries.

From: HBVRegDB: Annotation, comparison, detection and visualization of regulatory elements in hepatitis B virus sequences

Parameter Meaning blastn tblastx
-e Expectation value E 100 (10.0) 10(10)
-q Penalty for nucleotide mismatch -1 (-3) -
-r Reward for nucleotide match 1 (1) -
-E Cost to extend a gap -1 (-2) -2(1)
-G Cost to open a gap -2 (-5) -8(11)
-W K-tuple size 7 (11) 2(3)
  1. RefSeq Virus was chosen as the target database as the redundancy in Genbank makes the top matches less informative. The penalty for a mismatch, the cost to open and to extend a gap has been specifically set to detect distant similarity matches.
  2. BLOSUM62 was used for tblastx.