ALN 3.5.2 – Pairwise Alignment of Biological Sequences Supporting Spliced Alignment Procedures

ALN 3.5.2


Aln is a program for aligning a pair of nucleotide or amino acid sequences or groups of sequences. Aln accepts various combinations of distinct types of inputs: a single nucleotide sequence (SN), a single amino acid sequence (SA), a pre-aligned group of nucleotide sequences (MN), and a group of amino acid sequences (MA). Notably, aln can now perform mixed alignment between a nucleotide sequence and a protein sequence or a group of protein sequences [5]. This novel feature of aln enables us to predict eukaryotic gene structures (protein-coding exons) based on sequence homology with known protein sequence(s). The details of this procedure will be described in a later section entitled ‘Gene-structure prediction’.



Computational Biology Research Center (CBRC),




  • Linux
  • C++ compiler





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.

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