Searching the Composite Database
Keyword searching
OWL may be searched in a variety of ways: e.g., via keyword
searching of text,
author,
database code,
sequence fragment,
etc. - the information returned in the output from such queries may
be modified by changing the Qualifier switch provided. To build more
complex, and perhaps more useful, queries, simple keyword searches can be
combined using the logical operator functions provided by OWL's query
language, DELPHOS - the
type of queries to be combined may be specified using the Function
switch provided.
Similarity searching
By contrast with keyword searching, which is identity
matching, it is also possible to search OWL for sequence similarities.
Similarity measures are usually classified as global or
local. Global algorithms optimise the full alignment
of 2 sequences, which may include large dissimilar regions. Local
similarity algorithms focus on conserved subsequences, a single comparison
often yielding several alignments (dissimilar regions do
not contribute to the similarity measure). Local similarity tools, such as
BLAST, are
usually preferred for database searches, where cDNA's may be compared
with partially sequenced genes, or where distantly-related proteins may
share only isolated regions of similarity (e.g., in the vicinity of
an active site). Interpretation of
results is relatively straightforward, requiring one to identify
high-scoring sequences, or groups of sequences, with low probabilities that
such matches may have arisen by chance. Low scores with probabilities
tending to 1.0 indicate chance matches, as shown in the following
diagram
.
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