ggsearch query subject length ratio (sequence alignment)
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.
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?
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So, I figured out that you can use
-Mwhich controls the range of amino acid sequence lengths to be included in the search. For example,-M 100-200would 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.