BEAP: The BLAST Extension and Alignment Program- a tool for contig construction and analysis of preliminary genome sequence

Table 1 Bovine genes discovered in the Angus dwarfism locus by BEAP (prior to bovine assembly.)

Gene	Size¹	% Similarity to Human²	% of transcript retrieved³
ANTXR2	167.52 (3551)	90.6	29.7
ANXA3	58.69 (1443)	93.3	22.9
BMP2K	102.55 (2158)	91.0	35.5
BMP3	22.61 (1774)	89.4	47.9
COPS4	40.73 (1747)	93.7	100
FGF5	24.33 (5287)	89.8	100
FRAS1	486.29 (15213)	90.8	21.2
GDEP	34.2 (521)	86.0	100
GK2	1.67 (1677)	87.9	100
HEL308	48.50 (3559)	92.9	59.1
HNRPD	20.62 (2200)	95.1	100
HPSE	42.69 (3705)	93.3	66.4
MASA	24.63 (5113)	89.7	9.2
MRPL1	89.95 (1165)	89.9	24.6
PAQR3	21.48 (3990)	92.8	90.7
PLAC8	24.7 (1391)	-	0
PRDM8	24.04 (2536)	91.6	76.5
PRKG2	116.38 (3328)	94.6	100
SCD4	138.88 (1994)	90.1	100
THAP9	19.53 (3627)	90.0	13.8

¹The genomic sequence, introns and exons, is given in kilobases (kbs) and the (transcript size is presented in parenthesis, in bps). All data was queried in January of 2005, prior to completion of the bovine genome. The size estimates are based on human orthologs as found at UCSC genome browser at http://genome.ucsc.edu/
²The sequence similarity between human and bovine genes was determined by comparing exonic sequence only.
³The percentage of transcript retrieved by BEAP is based on the size of the human transcript.

ISSN: 1756-0500