Finds and displays all occurrences of a given target and/or
probe sequence within any specified 'PT_SERVER' database. The
species, targets and additional information are ranked and
displayed according to the degree of similarity.
Select a 'PT_SERVER' from the menu displayed after
pressing the 'PT_SERVER' button of the 'PROBE MATCH'
window.
Define whether similar (not perfectly matched) sites
should be displayed by pressing the 'Search depth'
button and selecting the number of mismatches (1 - 20)
from the menu.
Enable the 'Use weighted mismatches' toggle to use the
weights defined via 'EXPERT' button (see
´Weighting of Base Pairings´).
Define whether the species which contain the target or
probe (or similar) sequence should be marked (see
´What are Marked Species ?´) by enabling the 'Mark in database'
toggle.
Define if probe AND target sequence should be searched
by enabling the 'Check rev.compl. too' toggle.
Press the 'EXPERT' button to display the 'PD SPECIAL'
window if base pairings should be individually weighed
(see ´Weighting of Base Pairings´).
Press the 'MATCH' button to perform the search.
Enabling the 'Auto (match)' toggle will automatically
start a probe match whenever the target string is
changed. Try it when you design probes.
The results will be displayed within the display area,
ranked according to the degree of similarity between
probe string and database entries.
Brief description of the listed columns:
-
name: short name of the matched species
-
fullname: full name of the matched species
-
mis: number of mismatches
-
N_mis: number of pairings with ambiguous residues (N)
-
wmis: mismatch weights
-
pos: alignment position of match
-
rev: 0=normal match; 1=reverse complement match
Results from gene PT_servers consist of different columns:
-
organism: short name of the matched organism
-
genename: short name of the gene
-
mis, N_mis, wmis, rev (same meaning as with normal PT_server)
-
pos: position of match in genome sequence
-
gpos: position of match in gene sequence
Sequence sections containing stretches identical or
similar to the probe string or its reversed complement
are shown between dashes in the last column:
Perfectly matched positions are indicated by
double dashes, mismatches by base symbols. The
(hybrid destabilizing) quality of mismatches is
indicated by upper and lower case letters.
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