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SuiteMSA Version 1.3
New features in structural alignment display details
Update: 04-25-2012
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  New ranked data display:
In addition to secondary structure and transmembrane region information, SuiteMSA version 1.3 now allows for the display of any information ranked into up to ten levels showing '0' in lighter color and '9' in darker color. Two options are provided with a gradient of blue/green or red/yellow color. This display type is useful when structural properties can be represented quantitatively (e.g., disorderness or solvent accessibility).

Multiple structural displays can be opened under the MSA display (Figure 2.5). These displays may be individually closed by clicking on the "-" immediately under the file name. In order to help the navigation, selecting a position in one alignment display (for MSA or any structural alignments), will enlarge the characters in the corresponding positions in all alignment displays.

In Figure 1, for example, disorder prediction information is shown with the ranked data display with the MSA (top) as well as with the transmembrane prediction (bottom).
Figure 1: Structural information display from MSA Viewer. tax logo
Data conversion
In order to create this display, we converted the outputs from DisEMBL to rank-number sequences in FASTA format. The first portion of a DisEMBL output is shown below in figure 2. Using the values in the COILS column, and using the translation table as shown in table 2.1 we generated the rank-number sequence as shown figure 3. In this format, each amino acid is represented by a single integer (0-9). Note that any information that can be represented in up to ten categories for each residue (or nucleotide) can be displayed in this tool.
Figure 2: Raw ranked data. tax logo
Table: The translation of decimal values to 10 categories represented by integers. tax logo
Figure 3: Final translation in fasta format. tax logo