In the sample folder are available all input and output files used in this tutorial.
Supposing you have already found a template candidate, you need to align it against your target sequence. In this dummy example we take the sequences of two homologous proteins both endowed with 3D structure. That allow us to compare different type of alignments to the exact one derived from the structural alignment.
The two proteins are:
- Target = 2ANL (chain A)
- Template = 1DP5 (chain A)
This is the structural alignment:
The subali application let you choose from very different type of algorithms, strategies and parameters.
For testing purpose,
The fist step is to put the target and the template fasta sequences in a single file like that:
>target VLEEIAKDHGEALTI.... >template AFQVTSIPTLILFQ....
For more detail use the option -h with the subali application or see the AlignTest code.