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CHAPTER 9. VIEWING AND EDITING SEQUENCES
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Residue coloring
These preferences make it possible to color both the residue letter and set a background color
for the residue.
• Non-standard residues. For nucleotide sequences this will color the residues that are not
C, G, A, T or U. For amino acids only B, Z, and X are colored as non-standard residues.
Foreground color. Sets the color of the letter. Click the color box to change the color.
Background color. Sets the background color of the residues. Click the color box to
change the color.
• Rasmol colors. Colors the residues according to the Rasmol color scheme.
See http://www.openrasmol.org/doc/rasmol.html
Foreground color. Sets the color of the letter. Click the color box to change the color.
Background color. Sets the background color of the residues. Click the color box to
change the color.
• Polarity colors (only protein). Colors the residues according to the polarity of amino acids.
Foreground color. Sets the color of the letter. Click the color box to change the color.
Background color. Sets the background color of the residues. Click the color box to
change the color.
• Trace colors (only DNA). Colors the residues according to the color conventions of
chromatogram traces: A=green, C=blue, G=black, and T=red.
Foreground color. Sets the color of the letter.
Background color. Sets the background color of the residues.
Find
The Find function can also be invoked by pressing Ctrl + Shift + F (
+ Shift + F on Mac).
The Find function can be used for searching the sequence. Clicking the find button will search for
the first occurrence of the search term. Clicking the find button again will find the next occurrence
and so on. If the search string is found, the corresponding part of the sequence will be selected.
• Search term. Enter the text to search for. The search function does not discriminate
between lower and upper case characters.
• Sequence search. Search the nucleotides or amino acids. For amino acids, the single
letter abbreviations should be used for searching. The sequence search also has a set of
advanced search parameters:
Include negative strand. This will search on the negative strand as well.
Treat ambiguous characters as wildcards in search term. If you search for e.g. ATN,
you will find both ATG and ATC. If you wish to find literally exact matches for ATN (i.e.
only find ATN - not ATG), this option should not be selected.