Reconstruction of very short exons. Case A shows the result for the reconstruction of the human dynamitin (dynactin p50) gene, that contains a 3 amino acid exon and a following 2 amino acid exon that are differentially included in the final transcript. These exons could not be reconstructed with Blat and the old Scipio version, but using the new Scipio version that enables Needlman-Wunsch searches. The --exhaust_align_size parameter has been set to 15,000 bp because of the length of the intron. Case B shows the result of the reconstruction of the coronin gene from Puccinia graminis f. sp. tritici. The small but evolutionarily conserved exon 7 can now correctly be reconstructed. Case C shows the result of the reconstruction of the mouse dynactin p150 gene that contains three short exons of 7, 6, and 7 amino acids close to the 5'-end of the gene. For the correct reconstruction, the --exhaust_align_size parameter has been increased to 10,000 bp, because of the length of the intron, and the --exhaust_gap_size has been set to 21 because of the length of the query that could not be mapped. The colour coding of the scheme is the same as in Figure 3. For further information see Additional file 2.