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Model Specificities


[Long Terminal Repeat Library] [Genomic Repeat Library]

Long Terminal Repeat Library

Avian C-type LTR model

Nucleotides analyzed C-type
LTRs
known
"C-type
LTRs"
found
false neg. false pos.
Other Vertebrates (GenBank R. 99):
~ 29 million bp
25 31 0 <= 6
Other LTR types:
~ 43,000 bp
0 0 0 0
Yeast:
~ 24 million bp
0 15 0 15
E.coli:
~ 2.8 million bp
0 0 0 0



Mammalian C-type LTR model

Nucleotides analyzed C-type
LTRs
known
"C-type
LTRs"
found
false neg. false pos.
Mammalian (GenBank R. 92):
~ 113 million bp
25 28 0 <= 3*
Other LTR types:
~ 47,000 bp
0 0 0 0
Yeast:
~ 24 million bp
0 2 0 2
E.coli:
~ 2.8 million bp
0 0 0 0

* one of these new matches was subsequently shown to be biologically active as predicted -> this was a new true positive match!



Lentivirus LTR model

Nucleotides analyzed Lentivirus
LTRs
known
"Lentivirus
LTRs"
found
false neg. false pos.
HIV database (1995):
~ 4.3 million bp

HIV-1
HIV-2
SIV
AGM
MND
SYK
RELATED



52
14
22
17
1
2
17



54
14
22
17
2
2
17



0
0
0
0
0
0
0



<= 2
0
0
0
<= 1
0
0
Mammalian (GenBank R. 92):
~ 176 million bp
0 137 0 <= 137
Other LTR types:
~ 47,000 bp
0 0 0 0
Yeast:
~ 24 million bp
0 18 0 18
E.coli:
~ 2.8 million bp
0 6 0 6



Genomic Repeats Library

ALU model

Nucleotides analyzed Alus
known
"Alus"
found
false neg. false pos.
Full length Alus:
~ 1.6 million bp
5480 5333 147 0
Rodents (EMBL R. 59):
~ 67 million bp
0 37 0 37
Plants (EMBL R. 59):
~ 97 million bp
0 2 0 2



B1 model

Nucleotides analyzed B1
known
"B1"
found
false neg. false pos.
Full length B1:
~ 84,000 bp
482 410 72 0
Plants (EMBL R. 59):
~ 97 million bp
0 3 0 3



Primate THE model

Nucleotides analyzed THEs
known
"THEs"
found
false neg. false pos.
Full length THEs:
~ 23,000 bp
61 30 31 0
Plants (EMBL R. 59):
~ 97 million bp
0 1 0 1



L1 models

Nucleotides analyzed L1
known
"L1"
found
false neg. false pos.
L1 sequences > 300 bp:
~ 470,000 bp
576 396 180 0
Plants (EMBL R. 59):
~ 97 million bp
0 71 0 71