Table 4.

Predictions for chromosome 1

Public annotation	Totals	High confidence	Low confidence	No prediction
Forward strand
Protein function assigned	22	20	2	0
Conserved hypothetical	18	16	0	2
Hypothetical	13	9	3	1
Total	53	45	5	3
Reverse strand
Protein function assigned	9	8	1	0
Conserved hypothetical	18	14	4	0
Hypothetical	4	4	0	0
Total	31	26	5	0

Comparison of predicted splice sites with annotation of chromosome 1 of Leishmania major. A total of 84 genes have been annotated on chromosome 1 of L. major [12]. Of these, the method finds a splice site with a high-confidence score in all but 13 instances (85%). Only three genes were missed entirely by the method, with no prediction within the 400 nucleotide window upstream of the annotated start of the gene.