|-lopen||L PN||10.0||Local gap open|
|-lext||L PN||1.0||Local gap extend|
|-match||LG N||+1.0||Match score|
|-mismatch||LG N||-2.0||Mismatch score|
|-matrix filename||LG PN||BLOSUM62 (aa)
|Substitution matrix in NCBI BLAST format. See BLOSUM62 for an example.|
Gap penalties for global alignments
With global alignments, gap penalties are specified using the -gapopen and -gapext options. Up to 12 separate penalties can be specified: all combinations of query / target, left / interior / terminal, and open / extend can be assigned different penalties.
Default penalties are shown in the following table.
|Interior gap open||10.0 nucleotides, 17.0 proteins|
|End gap open||1.0|
|Interior gap extend||1.0|
|End gap extend||0.5|
The nucleotide defaults would be set using these options:
-gapopen 10.0I/1.0E -gapext 1.0I/0.5E
A numerical value for a penalty is optionally followed by one or more letters that specify particular types of gap. Here, "10.0I" means "Interior gap=10.0", and "1.0E" means "End gap=1.0". If no letters are given after the numerical value, then the penalty applies to all gaps. More than one letter can be specified, so for example "0.5IE" means "Interior and End gap=0.5", which is the same as all gaps. Following are valid letters: I=Interior, E=End, L=Left, R=Right, Q=Query and T=Target. If more than one numerical value is specified, then they must be separated by a slash character '/'. White space is not allowed. If a star (*) is used as the numerical value, then the gap is forbidden. Using * in an open penalty means that the gap will never be allowed, using * in an extension penalty means that gaps longer than one will be forbidden. So, for example, *LQ in -gapopen means "left end-gaps in the query are not allowed". A sign (plus or minus) is not allowed in the numerical value, which can be integer or floating-point (in which case a period '.' must be used for the decimal point). The -gapopen and -gapext options are interpreted first by setting the defaults, then by scanning the string left-to-right. Later values override previous values.