LAST for global pairwise alignment of DNA sequences

Question

[dustin.farkas.yo]

Hello,

I am trying to use LAST to perform a pairwise global alignment between two DNA sequences. Although LAST very quickly produces a MAF file containing local alignments, I am wondering if there is a way to automatically stitch the local alignments together to produce a global alignment.

Any guidance would be greatly appreciated! Thank you.

(LAST - http://last.cbrc.jp/)

Answer 1

[h.mon]

You are using the wrong software:

This program finds local alignments between query sequences, and reference sequences that have been prepared using lastdb.

However, you may try -T 1:

-T NUMBER

Type of alignment: 0 means "local alignment" and 1 means "overlap alignment". Local alignments can end anywhere in the middle or at the ends of the sequences. Overlap alignments must extend to the left until they hit the end of a sequence (either query or reference), and to the right until they hit the end of a sequence.

Warning: it's often a bad idea to use -T1. This setting does not change the maximum score drop allowed inside alignments, so if an alignment cannot be extended to the end of a sequence without exceeding this drop, it will be discarded.

Answer 2

[dustin.farkas.yo]

Thank you very much for your reply and suggestion! Unfortunately software such as LAST/MUMmer is the only kind I can find that can handle the 2mbp sequences I am trying to align. I was hoping that they could also perform global alignment as well. I will try your suggestion now.

[h.mon]

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