splicing-aware transcript-alignment to genomic DNA

 Spaln (space-efficient spliced alignment) is a stand-alone program that
 maps and aligns a set of cDNA or protein sequences onto a whole genomic
 sequence in a single job. It also performs spliced or ordinary alignment
 after rapid similarity search against a protein sequence database,
 if a genomic segment or an amino acid sequence is given as a query.
 .
 spaln supports a combination of protein sequence database and a
 given genomic segment and performs rapid similarity searches and
 (semi-)global alignments of a set of protein sequence queries against
 a protein sequence database. Spaln adopts multi-phase heuristics that
 makes it possible to perform the job on a conventional personal computer.