Minimium exon length in 2.3.3

[jwasmuth]

Hi, I am using spaln 2.2.3. I am getting some alignments with exons of length <5. In the github documentation, there is an option -yE but this is not in the help of spaln 2.3.3. I did try the option "-yE20" but I am still very short exons. I welcome any help. Thanks James

[ogotoh]

This parameter is internally used to help potentially best choice among a few heuristic algorithms, and it does not ensure that the resultant exon lengths are restricted to values larger than this parameter. Excessively fragmented gene structure is an indication that an inadequate parameter set is used. Please check the –T option whether you are using a proper species-specific parameter set. –LS option is sometimes helpful to prune out undesirable poorly predicted terminal exons.

[jwasmuth]

Thanks. The -T worked well in this instance. I'd also like to use spaln on a species (Giardia) for which there seems to be no parameter set, not one of a closely related species. Do you have instructions on how to build one?

[ogotoh]

Giardia genome appears to be intron-poor, so that only a small number of learning samples have been available. I think –T gairlamb (or equivalently –T Archamoe) works, but unfortunately it must be regarded as only a tentative one.