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

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

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)

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.
BLOSUM62 was used for tblastx.

ISSN: 1743-422X