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Last Update: 2006.05.16

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Example

III. Multiple Alignment

SHEBA can also compare one structure against many with different kinds of output. First, create a simple text file with a list of [*env] file names to be compared with (currently the program does not process a list of [*.pdb] file names). Name the text file with [*.list] extension and save at the same directory of those [*.env] files. Here is an example:

1. Convert [*.list] to [*.db] [back to Manual]

Use -D option to create a [*.db] file, a preprocessed binary file of [*.list], for faster processing of multiple alignment. Please note that if the SHEBA program is re-compiled, you have to re-run this option to get proper [*.db] file.

sheba -D test.list

Output:

2. One-to-Many Alignments with Insertion [back to Manual]

With -I option, the first structure in the [*.db] file (converted from [*.list] file) is aligned with all the structures in that file. A row formated output with inserstion is stored in another file with [*.I.out] extension in the same directory.

%sheba -I test.db

Output:

3. One-to-Many Alignments without Insertion: [back to Manual]

This -J option aligns the first structure in the [*.db] file (converted from [*.list] file) with the rest of the structures in that file. A row formated output without inserstion at the gaps is stored in another file with [*.J.out] extension in the same directory.

%sheba -J test.db

Output:

4. One-to-Many Alignments Summary-only Output [back to Manual]

There are two options for multiple alignments summary-only output and the results are the same. The input file can be [*.pdb] format or [*.env] format. The -A option takes [*.db] files and the output is stored in a file with [*.A.out] extension in the same directory. While -L option takes [*.list] file and the output file has [*.L.out] extension.

%sheba -A 1EVH.pdb test.db

Output:

%sheba -L 1EVH.pdb test.list [back to Manual]

Output: