Details
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Type:
New Feature
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Status: Open
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Priority:
Major
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Resolution: Unresolved
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Affects Version/s: None
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Fix Version/s: None
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Component/s: renderer
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Labels:None
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Mantis ID:12048
Description
Request from Greg Richmond (he should be the tester : g.s.richmond@dundee.ac.uk) for support of grey-scale colourschemes and box-shade style inverse video effects.
Completely conserved residues are shown as white letters on a black background, Completely unconserved is black text on a white background. Greyscale boxes are used for less conserved but similar regions.
From the additional information it is clear there are four user definable colouring states :
Totally Conserved
Identical (to consensus)
Conserved (similar to consensus)
Unconserved (different)
****** ADDITIONAL INFORMATION ******
From the boxshade faq:
http://www.ch.embnet.org/software/BOX_faq.html
How does the algorithm work ???
For some more details see the documentation file that comes with the BOXSHADE program or see BOX_doc.html
A brief description: In the first step, the program checks for every column in the alignment, if there are enough identical/similar residues to form a consensus (threshold can be defined by user).
In the second step, the program checks for every residue if it is identical or similar to the consensus of the corresponding alignment column. If there is no such consensus or the residue is neither identical nor similar to the consensus, this residue will be printed in normal rendition. If the residue is identical to the column-consensus, it will be printed in a special rendition (user-defined, usually inverse). If the residue is not identical but at least similar to the column-consensus, it will be printed in another user-defined rendition (usually on gray background). Positions in the alignment which are totally invariant can be treated specially.
Residue similarity is defined by a (editable) parameter file, not by any substitution matrix.
Completely conserved residues are shown as white letters on a black background, Completely unconserved is black text on a white background. Greyscale boxes are used for less conserved but similar regions.
From the additional information it is clear there are four user definable colouring states :
Totally Conserved
Identical (to consensus)
Conserved (similar to consensus)
Unconserved (different)
****** ADDITIONAL INFORMATION ******
From the boxshade faq:
http://www.ch.embnet.org/software/BOX_faq.html
How does the algorithm work ???
For some more details see the documentation file that comes with the BOXSHADE program or see BOX_doc.html
A brief description: In the first step, the program checks for every column in the alignment, if there are enough identical/similar residues to form a consensus (threshold can be defined by user).
In the second step, the program checks for every residue if it is identical or similar to the consensus of the corresponding alignment column. If there is no such consensus or the residue is neither identical nor similar to the consensus, this residue will be printed in normal rendition. If the residue is identical to the column-consensus, it will be printed in a special rendition (user-defined, usually inverse). If the residue is not identical but at least similar to the column-consensus, it will be printed in another user-defined rendition (usually on gray background). Positions in the alignment which are totally invariant can be treated specially.
Residue similarity is defined by a (editable) parameter file, not by any substitution matrix.