bl2seq

bl2seq

---

bl2seq (BLAST 2 Sequences) allows for the alignment of two given sequences.

An example of a bl2seq command-line entry:

bl2seq -p programname -i firstfilename -j secondfilename -o   <outputfilenanme>

The following table summarizes the bl2seq options.

Option	Definition	Type	Default
-a	SeqAnnot output file.	[File Out]
-d	Theoretical database size (0 is real size).	[Integer]	0
-e	Expectation value (E).	[Real]	10.0
-g	Gapped.	[T/F]	T
-i	First sequence.	[File In]
-j	Second sequence.	[File In]
-m	Use MegaBLAST for search.	[T/F]	F
-o	Alignment output file.	[File Out]	stdout
-p	Program name: blastp, blastn, blastx, tblastn, tblastx. For blastx, the first sequence should be nucleotide; for tblastn, the 2nd sequence sequence should be nucleotide.	[String]
-q	Penalty for a nucleotide mismatch (blastn only).	[Integer]	-3
-r	Reward for a nucleotide match (blastn only).	[Integer]	1
-t	Length of the largest intron allowed in tblastn for linking HSPs.	[Integer]	0
-A	Input sequences in the form of <accession.version>.	[T/F]	F
-D	Output format: 0 = traditional; 1 = tabulated.	[Integer]	0
-E	Cost to extend a gap (0 invokes default behavior).	[Integer]	0
-F	Filter query sequence (DUST with blastn, SEG with others)	[String]	T
-G	Cost to open a gap (0 invokes default behavior).	[Integer]	0
-I	Location on first sequence.	[String]
-J	Location on second sequence.	[String]
-M	Matrix.	[String]	BLOSUM62
-S	Query strands to search against database (blastn only). 3 is both, 1 is top, 2 is bottom.	[Integer]	3
-T	Produce HTML output.	[T/F]	F
-U	Use lowercase filtering for the query sequence.	[T/F]	F
-W	Wordsize (0 invokes default behavior).	[Integer]	0
-X	X dropoff value for gapped alignment (in bits) (0 invokes default behavior).	[Integer]	0
-Y	Effective length of the search space (use 0 for the real size).	[Real]	0