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Table 1 Benchmark comparison of ASPIC with other similar tools

From: ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences

  ASPIC ASAP ASD ACEVIEW
GENE #introns (#novel) #TS #EST/splice #introns (#ASPIC) #TS #introns (#ASPIC) #TS #introns (#ASPIC) #TS
ABCB10 12(0) 2 12.42 12(12) 1 Not Found   13(12) 3
ACADM 21(1) 15 31.52 15(14) 6 Not Found   22(20) 14
ACTN2 23(0) 28 19.09 20(20) 1 22(22) 4 23(23) 8
ADAM15 41(4) 67 40.07 13(13) 4 29(29) 11 56(37) 25
ADAMTS4 8(0) 3 8.63 7(7) 1 8(8) 4 8(8) 3
ADORA1 13(1) 10 4.69 8(8) 4 12(12) 9 10(9) 7
ADORA3 15(13) 5 6.13 2(2) 2 Not Found   3(2) 3
AGL 40(1) 12 14.48 38(38) 1 Not Found   39(39) 10
AGRN 41(4) 21 16.98 35(32) 1 Not Found   45(37) 11
AGT 7(2) 17 52.86 4(3) 1 Not Found   9(5) 8
AHCYL1 26(4) 35 48.50 19(19) 5 19(19) 4 26(22) 13
AKR7A2 9(1) 6 73.33 6(6) 1 7(7) 2 31(8) 15
ALDH9A1 17(4) 10 39.29 11(11) 2 Not Found   16(13) 7
ALPL 15(0) 8 19.47 14(13) 3 13(13) 3 17(15) 9
AMPD1 14(0) 4 7.64 13(13) 1 Not Found   45(14) 12
ANGPTL1 6(0) 3 10.50 5(5) 1 Not Found   6(6) 4
ANGPTL3 6(0) 5 19.17 6(6) 2 Not Found   8(6) 7
ANXA9 15(1) 3 14.40 13(13) 1 14(13) 2 16(14) 6
AP4B1 18(0) 22 14.61 12(12) 1 17(16) 12 16(16) 14
APCS 2(1) 5 62.50 1(1) 1 Not Found   1(1) 1
ARHGEF2 32(1) 37 15.19 22(22) 3 26(25) 6 35(31) 17
ARHGEF11 47(1) 9 7.70 42(42) 2 41(40) 6 46(45) 17
ARHGEF16 14(2) 12 18.64 10(10) 1 Not Found   15(12) 5
ARNT 26(1) 14 11.73 20(18) 1 22(21) 3 38(26) 14
ARPC5 4(1) 2 120.75 3(3) 1 4(2) 2 6(3) 4
ARTN 8(0) 10 5.25 7(7) 4 6(6) 3 7(7) 10
ATAD3A 22(2) 10 36.41 16(16) 2 Not Found   58(21) 27
ATP1B1 11(2) 12 59.27 7(7) 1 10(9) 4 11(8) 10
ATP2B4 29(3) 11 8.07 22(22) 5 23(23) 3 26(26) 14
Clorf10 2(0) 1 7.00 2(2) 1 Not Found   2(2) 2
Clorf26 22(0) 7 7.91 17(17) 1 Not Found   23(22) 6
C1QB 3(1) 3 25.67 5(2) 3 5(2) 3 6(2) 5
CAPZA1 15(4) 15 68.40 11(11) 2 10(9) 3 12(11) 7
CTRC 9(1) 4 36.22 8(8) 1 Not Found   8(7) 3
DMRTA2 2(0) 2 1.00 1(1) 1 Not Found   2(2) 1
DPH2L2 12(1) 11 31.25 10(10) 7 12(11) 12 12(11) 14
EPHA2 20(1) 8 13.45 16(16) 1 17(17) 7 20(19) 8
EYA3 20(0) 9 11.40 15(15) 1 Not Found   21(20) 10
FBXO2 9(0) 6 13.67 9(8) 2 6(5) 3 9(8) 5
FCGR3B 7(0) 5 22.57 4(4) 1 Not Found   7(7) 6
FUCA1 11(3) 8 18.00 8(8) 2 Not Found   7(7) 2
GBP2 17(3) 8 27.82 12(12) 2 Not Found   26(14) 10
GMEB1 12(1) 5 16.67 9(9) 2 11(11) 3 11(11) 6
HNRPR 20(2) 38 45.70 16(15) 7 12(12) 7 21(18) 17
LGALS8 22(2) 25 16.00 12(11) 4 13(13) 4 27(19) 21
LRRN5 3(0) 3 3.00 5(3) 2 Not Found   5(3) 4
LYPLA2 15(0) 14 96.07 14(14) 6 Not Found   15(14) 14
MASP2 11(0) 5 7.00 11(11) 2 11(11) 5 11(11) 6
MOV10 35(4) 42 25.29 29(29) 7 24(23) 8 33(31) 21
NPPB 2(0) 1 30.50 2(2) 1 Not Found   3(2) 3
PAFAH2 18(3) 11 15.06 12(11) 2 13(13) 5 16(14) 8
PALMD 8(0) 9 35.63 7(7) 1 Not Found   9(8) 8
PEX10 12(1) 13 21.58 6(6) 1 10(10) 7 12(10) 11
PINK1 10(2) 15 40.20 7(7) 2 Not Found   9(8) 10
PTPRU 38(3) 15 12.89 20(20) 1 Not Found   35(35) 9
RHOC 17(3) 5 8.35 13(2) 7 15(1) 9 39(14) 31
SDC3 6(2) 5 5.33 4(3) 2 8(4) 5 9(5) 6
SDHB 11(0) 12 97.27 9(9) 3 Not Found   13(11) 11
SERPINC1 12(2) 7 18.75 8(8) 2 8(8) 3 16(10) 11
SFPQ 12(3) 11 74.75 9(9) 1 9(9) 3 17(9) 25
TARDBP 21(3) 20 29.38 15(13) 4 9(9) 4 18(16) 15
TCN2 13(1) 10 26.15 9(9) 2 12(12) 4 13(10) 11
TOR3A 15(2) 9 19.20 9(9) 4 11(11) 8 15(13) 12
VAMP3 5(0) 3 80.60 6(5) 2 6(5) 3 7(5) 10
Total 1009(94) 11.9 28.3 753(721) 2.3 495(461) 5.1 1194(905) 9.7
  1. ASPIC results from a random sample of 64 human genes from Chromosome 1 compared to those from the ASAP, ASD and AceView resources. The first column reports the HUGO name of the examined gene. The ASPIC data include the total number of predicted introns (novel introns in brackets), the minimum number of compatible transcripts and the average number of ESTs supporting gene splices. Introns with 2 non canonical splices are accepted by ASPIC only if confirmed by at least two ESTs. For the other resources the number of predicted introns (in brackets those also predicted by ASPIC) and the minimum number of compatible transcripts are reported. Other resources: AceView (July 2003 and August 2004 releases), ASD (July 2004) and ASAP (July 2004).