ggsearch query subject length ratio (sequence alignment)

Question

[comacke]

Using the ggsearch program (part of the fasta package) to produce some global alignments.

Here I read that in ggsearch alignments are only performed if the subject is within 80% to 120% of the query length.

All Pairs Similarity Search Under A Substitution Matrix For A Large Number Of Short Protein Sequences (Hamish's answer)

Here it says between 80 and 125%. This would make more sense as it would be symmetric if you switched query and subject.

http://www.biomedcentral.com/content/supplementary/1471-2105-13-42-s1/Cloud-BioLinux-Package-Documentation/docs/ggsearch.html

When I look at my own results, all the aligned sequences are between 70% and 130% of the query length. Just curious how this range is determined. Would also like to know if there is a parameter that can change this range?

[comacke]

So, I figured out that you can use -M which controls the range of amino acid sequence lengths to be included in the search. For example, -M 100-200 would only perform searches on sequences with lengths between 100 and 200 (inclusive). I'd still like to know how the default setting (without the -M option) is determined.