Download Bioinformatics Toolbox

blastncbi
Description
MatrixValue
Property to select a substitution matrix
for amino acid sequences. Enter 'PAM30’,
'PAM70', 'BLOSUM80', 'BLOSUM62', or
'BLOSUM45’. The default value is 'BLOSUM62'.
InclusionValue
Property for PCI-BLAST searches to define
the statistical significance threshold. The
default value is 0.005.
PctValue
Property to select the percent identity. Enter
None, 99, 98, 95, 90, 85, 80, 75, or 60. Match
and mismatch scores are automatically
selected. The default value is 99 (99, 1, -3)
The Basic Local Alignment Search Tool (BLAST) offers a fast and
powerful comparative analysis of interesting protein and nucleotide
sequences against known structures in existing online databases.
blastncbi(Seq, Program) sends a BLAST request against a sequence
(Seq) to NCBI using a specified program (Program).
• With no output arguments, blastncbi returns a command window
link to the actual NCBI report.
• A call with one output argument returns the Report ID (RID)
• A call with two output arguments returns both the RID and the
Request Time Of Execution (RTOE, an estimate of the time until
completion)
blastncbi uses the NCBI default values for the optional arguments:
'nr' for the database, 'L' for the filter, and '10' for the expectation
threshold. The default values for the remaining optional arguments
depend on which program is used. For help in selecting an appropriate
BLAST program, visit
http://www.ncbi.nlm.nih.gov/BLAST/producttable.shtml
Information for all of the optional parameters can be found at
6-25