3.4 'Blast 2 sequences' page

'Blast 2 sequences' program was initially written by Tatiana Tatusova and Tom Madden []. The standalone wwwblast version of the program resembles the 'Align two sequences' service from the NCBI BLAST home page. It is a quick way to directly compare two sequences without going through the database formatting step. We list the parameters accepted by this web form in the table below since they are different from those accepted by other web forms in the package.

Table 3.4 URLAPI parameters specific to 'BLAST 2 Sequences' web form
Parameters	Function/Value
program	Specifies the type of BLAST searches: blastn, blastp, tblastn, blastx, or tblastx
one	The first sequence
from	Optional, start of the subsequence position on the first sequence
to	Optional, end of the subsequence position on the first sequence
seqfile1	Path and file name for the first sequence, not to be used with 'one'
two	The second sequence
ffrom	Optional, start of the subsequence position on the second sequence
tto	Optional, end of the subsequence position on the second sequence
seqfile2	Path and file name for the second sequence, not to be used with 'two'
Matrix	Protein scoring matrix to use: 0, 1, 2, 3, 4 *
match	match reward for nucleotide search (1)
msmatch	mismatch penalty for nucleotide search (-2)
gopen	gap open penalty **
gext	gap extension penalty **
dropoff	X-dropoff for alignment extension (50)
expect	Expect value cutoff
word	word size
filter	1 = on , 0 = off

Note: Further information on these marked parameters:

* 0 - BLOSUM62; 1 - PAM30; 2 - PAM70; 3 - PAM45; 4 - BLOSUM80

** For more information see: http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node89.html.