Biomedical Engineering Reference
In-Depth Information
Executing a BLAST search for a pattern match involves simply filling out the template depicted in
Figure 8-14
. The search string representing the nucleotide sequence to be searched for is entered, in
FASTA format, in the "Search" field. The entire string can be used in the search, or only a subset of
the string. To use a subset, the researcher enters the subset sequence locations in the "From" and
"To" fields of the "Set subsequence" area. For example, to limit matches to the region in the search
string from nucleotide 10 to nucleotide 20, the researcher would enter "From" = 10 and "To" = 20.
The default search includes the entire search string.
The only other parameter that must be defined for a basic BLAST search is the database to use for
the search. Database options available through a pull-down menu include, among others, "nr" (all
GenBank, EMBL, DDBJ, and PDB sequences), "est" (GenBank, EMBL, and DDBJ sequences from EST
Divisions), "pat" (nucleotides from the Patent division of GenBank), "pdb" (sequences derived from
the 3D structures in the Protein Data Bank), and "month" (all new or revised GenBank, EMBL, DDBJ,
and PDB sequences released in the last 30 days).
Options are also available for advanced searches, as shown in the bottom half of
Figure 8-14
. The
"Limit by entrez query" option allows BLAST searches to be limited to the results of an Entrez query
against the selected database. Because Entrez supports a powerful query engine, the search can be
significantly narrowed through an Entrez query. Alternatively, the search can be limited to one of
several dozen organisms from a pull-down menu.
The "Choose filter" option enables masks for low compositional complexity, human repeats, lookup
table, and lowercase characters in the search sequence; all or none of these options can be selected.
