seq.alg – Algorithms for Sequences¶

ost.seq.alg.MergePairwiseAlignments(pairwise_alns, ref_seq)¶

Merge a list of pairwise alignments into a multiple sequence alignments. This function uses the reference sequence as the anchor and inserts gaps where needed. This is also known as the star method.

The resulting multiple sequence alignment provides a simple way to map between residues of pairwise alignments, e.g. to compare distances in two structural templates.

There are a few things to keep in mind when using this function:

• The reference sequence mustn’t contain any gaps
• The first sequence of each pairwise alignments corresponds to the reference sequence. Apart from the presence of gaps, these two sequences must be completely identical.
• If the reference sequence has an offset, the first sequence of each pairwise alignment must have the same offset. This offset is inherited by the first sequence of the final output alignment.
• The resulting multiple sequence alignment is by no means optimal. For better results, consider using a multiple-sequence alignment program such as MUSCLE or ClustalW.
• Residues in columns where the reference sequence has gaps should not be considered as aligned. There is no information in the pairwise alignment to guide the merging, the result is undefined.