Gotoh, O. (2000) " Homology-based gene structure prediction: simplified matching algorithm by the use of translated codon (tron) and improved accuracy by allowing for long gaps." Bioinformatics,16, 190-202.
 Gotoh, O., Morita, M., Ichiyoshi, N., and Yada, T. (2005) Discovery of protein coding genes through chromosome-to-chromosome sequence comparison. Genome Informatics 2005, Yokohama, 12.19-21.
% alngg -I1 S1.seq -I2 S2.seqBut you can not catch anything for the result with this run. It is necessary for any outputs with the below options.
[Output Options] -O1gtf Out_file Predictions for Seq1(GTF) -O2gff Out_file Predictions for Seq2(GFF) -Ogene Out_file Output for GUI -Ocluster Out_file Output for Synteny mapIf you want to compare with the partial sequence, the following options are suited.
-I1Start NNN the comparison starts from NNN of Seq1 -I1End NNN the comparison terminates to NNN of Seq1 -I2Start NNN the comparison starts from NNN of Seq2 -I2End NNN the comparison terminates to NNN of Seq2Alngg detects the same strand genes. If you want to get the reverse strand genes, run with the following option.
-rev the comparison with the reverse Seq2Alngg is a homology base system. it sometimes lose the first or last exon because of the weak match. If you want to change the default, you can specify the following options.
-completeGene try to extract the lost first exon or last exon again.By this option the performance would go down under the influence of unreliable matches.
Copyright © 1997-2007 Osamu Gotoh