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The Spliced Alignment Problem (SAP) that consists in finding an optimalsemi-global alignment of a spliced RNA sequence on an unspliced genomicsequence has been largely considered for the prediction and the annotation ofgene structures in genomes. Here, we re-visit it for the purpose of identifyingCDS ortholog groups within a set of CDS from homologous genes and for computingmultiple CDS alignments. We introduce a new constrained version of the splicedalignment problem together with an algorithm that exploits full information onthe exon-intron structure of the input RNA and gene sequences in order tocompute high-coverage accurate alignments. We show how pairwise splicedalignments between the CDS and the gene sequences of a gene family can bedirectly used in order to clusterize the set of CDS of the gene family into aset of ortholog groups. We also introduce an extension of the spliced alignmentproblem called Multiple Spliced Alignment Problem (MSAP) that consists inaligning simultaneously several RNA sequences on several genes from the samegene family. We develop a heuristic algorithmic solution for the problem. Weshow how to exploit multiple spliced alignments for the clustering ofhomologous CDS into ortholog and close paralog groups, and for the constructionof multiple CDS alignments. An implementation of the method in Python isavailable on demande to SFA@USherbrooke.ca.  Keywords: Spliced alignment, CDS ortholog groups, Multiple CDS alignment,Gene structure, Gene family.

Improving spliced alignment for identification of ortholog groups and multiple CDS alignment