DNA/RNA Sequence Alignment

Question

[Mirza]

Is there any field in bioinformatics where global sequence alignment is used only for sequences with the same length?

[Ram]

This looks like an XY question. What is the purpose behind your asking this question - as in, why do you have this question?

[Mirza]

I am doing a research on one new method of optimizing sequence alignment process (Needleman - Wunsch algorithm) but the idea would only work with sequence that have the same length. I am wondering if that will have any real-life utilization. Precisely, how often do we have those situations where we are aligning same-length sequences.

[Mensur Dlakic]

I don't want to say that identical sequence lengths never happen, but is so rare that for practical purposes one could say it never happens. Even two strains of the same bacterial species will not have an identical number of basepairs. Heck, the same strain sequenced twice from different starting DNA material could assemble with different sizes.