Can NUCmer align a short sequence with a much longer sequence (local alignment)?

Question

[nchuang]

Hey guys,

I wrote a script in python to call nucmer to align a query sequence with a 10k nucleotide sequence. The query sequence size varies from 20 bases to as large as 2000 bases. It seems like nucmer will find a match with the larger sized queries but it can't with smaller. Is this just not what nucmer/mummer is designed to do and I should just stick with using Smith-Waterman?

Thanks!

[natasha.sernova]

I would try MAFFT7.

http://mafft.cbrc.jp/alignment/software/algorithms/algorithms.html

" Updated! (2015/Jun) Parameters for E-INS-i have been changed in version 7.243. The new parameters work better for aligning a set of long sequences and short sequences that are closely related to each other. To disable this change, add the --oldgenafpair option.

With the new parameters, E-INS-i may be able to align multiple cDNAs and multiple genomic sequences of a gene from closely related species. However, it consumes large memory space when the sequences are long. "

[nchuang]

oh I guess that's another option. I was hoping to keep all the code I wrote for NUCmer reading/parsing. I liked how Mummer spits out a coordinate file.

Answer 1

[nchuang]

I figured it out!

you have to set the minimum cluster size -c to as small as the query you are using. The default is 65.