ogotoh

Dear Min-Jin, I am trying a larger scale test to find when spaln fails. Please wait a while till I can figure out the source of the trouble. Because of...

Dear Min-Jin, I have just uploaded new version of spaln ver3.0.0. Compared with previous versions, the computation speed has been considerably improved, partly due to modified algorithms and vectorization. For...

1. The expected gene size with intron (Expected_Max_Gene_Size) should be assigned. When the genome size (Genome_Size) is known, spaln simply estimates Expected_Max_Gene_Size ~= sqrt(Genome_Size). Underestimation of Expected_Max_Gene_Size can cause serious...

I made a mistake in 1. Actually, Expected_Max_Gene_Size ~= Const * sqrt(Genome_Size), where Const is empirically determined to be 36.

I made a mistake in 1. Actually, Expected_Max_Gene_Size ~= Const * sqrt(Genome_Size), where Const is empirically determined to be 36.

Yes, that's right.

Dear Andreas, As explained in my paper “Homology-based gene structure prediction: simplified matching algorithm using a translated codon (tron) and improved accuracy by allowing for long gaps” (O. Gotoh, Bioinformatics,...

Sortgrcd does not support –O1 option, because *.erd, *.grd, and *.qrd files produced with spaln –O12 option do not contain alignment (indel) information. You must run spaln with –O1 option...

This message is displayed when you have not yet formatted your genomic sequence. Follow the instruction of this GitHub README.md for formatting. Typically, you may run spaln in the directory...

Thank you for your report, according to which I can figure out the cause of the error. Looking into the error message you provided, the problem seems to reside in...