  The Spliced Alignment Problem (SAP) that consists in finding an optimal
semi-global alignment of a spliced RNA sequence on an unspliced genomic
sequence has been largely considered for the prediction and the annotation of
gene structures in genomes. Here, we re-visit it for the purpose of identifying
CDS ortholog groups within a set of CDS from homologous genes and for computing
multiple CDS alignments. We introduce a new constrained version of the spliced
alignment problem together with an algorithm that exploits full information on
the exon-intron structure of the input RNA and gene sequences in order to
compute high-coverage accurate alignments. We show how pairwise spliced
alignments between the CDS and the gene sequences of a gene family can be
directly used in order to clusterize the set of CDS of the gene family into a
set of ortholog groups. We also introduce an extension of the spliced alignment
problem called Multiple Spliced Alignment Problem (MSAP) that consists in
aligning simultaneously several RNA sequences on several genes from the same
gene family. We develop a heuristic algorithmic solution for the problem. We
show how to exploit multiple spliced alignments for the clustering of
homologous CDS into ortholog and close paralog groups, and for the construction
of multiple CDS alignments. An implementation of the method in Python is
available on demande to<EMAIL_ADDRESS>  Keywords: Spliced alignment, CDS ortholog groups, Multiple CDS alignment,
Gene structure, Gene family.
