Supposing you have already found a good template, now you need to align it against your target sequence. The subali application let you choose from very different type of algorithms, strategies and parameters.
- Sequence to sequence
- Profile to sequence
- Profile to profile
Weighting scheme (only for profiles):
- PSIC (Sunyaev et al., 1999)
- Henikoff (Henikoff & Henikoff, 1994)
- SecDivergence (Rychlewski et al., 2000)
- Sum of pairs
- Dot product
- EDistance (Euclidean distance)
- Atchley metric
Blosum substitution matrix:
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.