Alignment Class

[grabear]

Decide on different alignment strategies that we would like to be able to employ.

• Filtered Sequence Alignment
  • Amino Acid Alignment with multiple GUIDANCE2 iterations.
  • Nucleic Acid Alignment without filtered sequences using PAL2NAL.
    • Catch PAL2NAL errors and remove sequences that aren't working
      • Employ the Filtered Column Alignment strategy for the sequences that aren't working by aligning multiple query sequences (Homo_sapiens, Macaca_mulatta, Mus_musculus) with the "bad" sequences.
• Solitary Alignment
  • CLUSTAL Omega
  • PAL2NAL
• Filtered Column Alignment
  • For sequences that are more cluttered, deploy a strategy for safely removing "bad" columns from the alignments by using GUIDANCE2
  • Use PAL2NAL on what's left.

[sdhutchins]

💪

[grabear]

Here the general format for the class will be to create functions that call the alignment program of interest.

class Alignment(GenBank):
def clustal_omega(self)
def guidance2(self)
def pal2nal(self)

From here we can create other useful classes such as...
class FilteredAlignment(Alignment)
def aa_guidance(self)
def na_pal2nal(self)

These are all just bad examples, but it will allow us to be more versatile with our strategies in the future.

[sdhutchins]

@datasnakes/snakes hello. I think it makes a ton of sense tbh.