HUMOPS: NetGene splice site prediction
virus mail server
netgene at virus.fki.dth.dk
Fri Mar 20 07:30:41 EST 1992
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NetGene
Neural Network Prediction of Splice Sites
Reference:
Brunak, S., Engelbrecht, J., and Knudsen, S. (1991). Prediction of
Human mRNA donor and acceptor sites from the DNA sequence. Journal of
Molecular Biology 220:49-65.
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Report ERRORS to Jacob Engelbrecht engel at virus.fki.dth.dk.
Potential splice sites are assigned by combining output from a local and
a global network. The prediction is made with two cutoffs: 1) Highly
confident sites (no or few false positives, on average 50% of the true
sites detected); 2) Nearly all true sites (more false positives - on
average of all positions 0.1% false positive donor sites and 0.4% false
positive acceptor sites, at 95% detection of true sites). The network
performance on sequences from distantly related organisms has not been
quantified. Due to the non-local nature of the algorithm sites closer
than 225 nucleotides to the ends of the sequence cannot be assigned.
Column explanations, field identifiers:
POSITION in your sequence (either first or last base in intron).
Joint CONFIDENCE level for the site (relative to the cutoff).
EXON INTRON gives 20 bases of sequence around the predicted site.
LOCAL is the site confidence from the local network.
GLOBAL is the site confidence from the global network.
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The sequence: HUMOPS contains 6953 bases, and has the following composition:
A 1524 C 2022 G 1796 T 1611
1) HIGHLY CONFIDENT SITES:
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ACCEPTOR SITES:
POSITION CONFIDENCE INTRON EXON LOCAL GLOBAL
4094 0.27 TGTCCTGCAG^GCCGCTGCCC 0.63 0.66
5167 0.20 TGCCTTCCAG^TTCCGGAACT 0.59 0.64
3812 0.17 CTGTCCTCAG^GTACATCCCC 0.68 0.54
3164 0.02 TCCTCCTCAG^TCTTGCTAGG 0.79 0.32
2438 0.01 TGCCTTGCAG^GTGAAATTGC 0.78 0.33
DONOR SITES:
POSITION CONFIDENCE EXON INTRON LOCAL GLOBAL
3979 0.38 CGTCAAGGAG^GTACGGGCCG 0.92 0.74
2608 0.17 GCTGGTCCAG^GTAATGGCAC 0.85 0.54
4335 0.06 GAACAAGCAG^GTGCCTACTG 0.83 0.41
2) NEARLY ALL TRUE SITES:
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ACCEPTOR SITES:
POSITION CONFIDENCE INTRON EXON LOCAL GLOBAL
4094 0.55 TGTCCTGCAG^GCCGCTGCCC 0.63 0.66
3812 0.52 CTGTCCTCAG^GTACATCCCC 0.68 0.54
3164 0.49 TCCTCCTCAG^TCTTGCTAGG 0.79 0.32
5167 0.49 TGCCTTCCAG^TTCCGGAACT 0.59 0.64
2438 0.48 TGCCTTGCAG^GTGAAATTGC 0.78 0.33
4858 0.39 TCATCCATAG^AAAGGTAGAA 0.77 0.20
3712 0.36 CCTTTTCCAG^GGAGGGAATG 0.88 -0.01
4563 0.33 CCCTCCACAG^GTGGCTCAGA 0.81 0.05
5421 0.33 TTTTTTTAAG^AAATAATTAA 0.75 0.13
3783 0.29 TCCCTCACAG^GCAGGGTCTC 0.64 0.26
3173 0.25 GTCTTGCTAG^GGTCCATTTC 0.52 0.36
4058 0.24 CTCCCTGGAG^GAGCCATGGT 0.43 0.51
1784 0.22 TCACTGTTAG^GAATGTCCCA 0.68 0.08
6512 0.21 CCCTTGCCAG^ACAAGCCCAT 0.67 0.08
2376 0.20 CCCTGTCTAG^GGGGGAGTGC 0.61 0.16
1225 0.18 CCCCTCTCAG^CCCCTGTCCT 0.65 0.07
1743 0.13 TTCTCTGCAG^GGTCAGTCCC 0.62 0.03
3834 0.13 GGGCCTGCAG^TGCTCGTGTG 0.26 0.58
4109 0.13 TGCCCAGCAG^CAGGAGTCAG 0.29 0.54
6557 0.13 CATTCTGGAG^AATCTGCTCC 0.56 0.12
1638 0.11 CCATTCTCAG^GGAATCTCTG 0.62 0.00
247 0.10 GCCTTCGCAG^CATTCTTGGG 0.55 0.11
6766 0.09 CTATCCACAG^GATAGATTGA 0.64 -0.06
906 0.08 AATTTCACAG^CAAGAAAACT 0.61 -0.02
6499 0.08 CAGTTTCCAG^TTTCCCTTGC 0.55 0.06
378 0.07 GTACCCACAG^TACTACCTGG 0.24 0.52
3130 0.07 CTGTCTCCAG^AAAATTCCCA 0.51 0.12
4272 0.07 ACCATCCCAG^CGTTCTTTGC 0.58 0.00
4522 0.07 TGAATCTCAG^GGTGGGCCCA 0.51 0.12
5722 0.07 ACCCTCGCAG^CAGCAGCAAC 0.55 0.05
2316 0.06 CTTCCCCAAG^GCCTCCTCAA 0.40 0.27
2357 0.06 GCCTTCCTAG^CTACCCTCTC 0.39 0.28
2908 0.06 TTTGGTCTAG^TACCCCGGGG 0.51 0.10
4112 0.06 CCAGCAGCAG^GAGTCAGCCA 0.25 0.50
1327 0.05 TTTGCTTTAG^AATAATGTCT 0.52 0.06
844 0.04 GTTTGTGCAG^GGCTGGCACT 0.62 -0.11
1045 0.04 TCCCTTGGAG^CAGCTGTGCT 0.54 0.01
1238 0.03 CTGTCCTCAG^GTGCCCCTCC 0.50 0.06
2976 0.03 CCTAGTGCAG^GTGGCCATAT 0.62 -0.12
3825 0.03 CATCCCCGAG^GGCCTGCAGT 0.16 0.60
1508 0.02 TGAGATGCAG^GAGGAGACGC 0.43 0.16
2257 0.02 CTCTCCTCAG^CGTGTGGTCC 0.53 0.00
5712 0.02 ATCCTCTCAG^ACCCTCGCAG 0.51 0.05
2397 0.00 CCCTCCTTAG^GCAGTGGGGT 0.41 0.16
4800 0.00 CATTTTCTAG^CTGTATGGCC 0.47 0.07
5016 0.00 TGCCTAGCAG^GTTCCCACCA 0.59 -0.11
DONOR SITES:
POSITION CONFIDENCE EXON INTRON LOCAL GLOBAL
3979 0.75 CGTCAAGGAG^GTACGGGCCG 0.92 0.74
2608 0.51 GCTGGTCCAG^GTAATGGCAC 0.85 0.54
4335 0.38 GAACAAGCAG^GTGCCTACTG 0.83 0.41
656 0.32 ACCCTGGGCG^GTATGAGCCG 0.56 0.66
5859 0.11 ACCAAAAGAG^GTGTGTGTGT 0.85 0.07
4585 0.09 GCTCACTCAG^GTGGGAGAAG 0.86 0.03
1708 0.06 TGGCCAGAAG^GTGGGTGTGC 0.85 0.01
6196 0.05 CCCAATGAGG^GTGAGATTGG 0.86 -0.01
667 0.03 TATGAGCCGG^GTGTGGGTGG 0.23 0.71
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