Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species

Table 1 Sequences tested in comparative analysis.

Species	typ. target size (kbp)	# of target sequences	# of query sequences
Bombyx mori p50T	2.8	213 289	8
Drosophila simulans	9.4	31 198	37
Bombyx mori str. Dazao	14	66 482	32
Nasonia vitripennis (contigs)	27	26 605	35
Nasonia vitripennis (scaffolds)	1 827	6 181	35
Drosophila sechellia	70	21 425	38
Aedes aegypti	113	36 206	40
Daphnia pulex	825	9 080	42
Anopheles gambiae	6 969	69 724	37
Drosophila melanogaster	21 575	13	38
Aspergillus niger	2 409	143	15
Homo sapiens	153 287	24	40
Macaca mulatta	150 724	22	40

A list of 9 insect, one fungi, and two primate genomes, searched for kinesin and myosin genes to compare the performance of Scipio with that of BLAT and Exonerate. Genomic target sequences were taken from different stages of assembly, as can be seen from the different typical target sizes (D. melanogaster, H. sapiens and M. mulatta were given as sets of complete chromosomes; of the genome of N. vitripennis, two versions were compared; the genome of A. gambiae was given partly in chromosomes, partly in small contigs). The protein query sequences were taken from the same species as the genome.

ISSN: 1471-2105