Index

OTHER_ADVANCED

Descr:	Other advanced options
Values:	A string combining the options:
	-G Cost to open a gap, see GAPCOSTS
	-E Cost to extend a gap, see GAPCOSTS
	-r Reward for match, see NUCL_REWARD
	-q Penalty for mismatch, see NUCL_PENALTY
	-e Expectation value (E), see EXPECT
	-W Word size, see WORD_SIZE
	-y Dropoff (X) for blast extensions in bits (default if zero)
	(Integer) default = 20 for nuc-nuc 7 for other programs
	Not applicable for megablast
	-X X dropoff value for gapped alignment (in bits) (Integer)
	default = 30 for nuc-nuc (blastn and megablast), 15 for other programs
	-Z Final X dropoff value for gapped alignment (in bits)
	(Integer) 50 for nuc-nuc (blastn), 25 for other programs
	megablast - not applicable
	-P 0 for multiple hits 1-pass, 1 for single hit 1-pass (Integer)
	Does not apply to blastn or megablast
	-A Multiple Hits window size (zero for single hit algorithm)(Integer)
	-I Number of database sequences to save hits for,
	see HITLIST_SIZE
	-b Number of database sequences to show alignments for,
	see ALIGNMENTS
	-v Number of database sequences to show one-line descriptions for,
	see DESCRIPTIONS
	-Y Effective length of the search space, see SEARCHSP_EFF
	-z Effective length of the database (use zero for the real size)(Real), default=0
	-c Pseudocount constant for PSI-BLAST (Integer), default=7
	-F Filtering directives, see FILTER
Default:	empty
Commands:	Put