|
methBLAST results of a panel of assays from methPrimerDB (1–12) and literature (13–14). |
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| Best hit when both primers align on correct target |
First misalignment |
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| # |
ID |
Assay type |
Gene symbol |
Sequence identifier |
Score (bits) |
E value |
Sequence identifier |
Score (bits) |
E value |
|
|
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| 1 |
14 |
BiPS |
VHL |
gb|L15409.1| [BISUL_METH_RC] |
40.1 (20) |
0.32 |
dbj|D64176.1| [BISUL_METH_RC] |
32.2 (16) |
79 |
| 2 |
236 |
BiPS |
NKX3-1 |
gb|U91540.1| [BISUL_UNMETH_FW] |
46.1 (23) |
0.007 |
dbj|AP005361.2| [BISUL_UNMETH_RC] |
44.1 (22) |
0.026 |
| 3 |
26 |
Ms-SNuPE |
RARB |
emb|X56849.1| [BISUL_UNMETH_FW] |
44.8 (22) |
0.015 |
dbj|AP001217.3| [BISUL_UNMETH_RC] |
40.8 (20) |
0.25 |
| 4 |
28 |
Ms-SNuPE |
CDKN2A |
dbj|AB060808.1| [BISUL_UNMETH_RC] |
46.1 (23) |
0.007 |
emb|AL590456.5| [BISUL_UNMETH_RC] |
40.1 (20) |
0.41 |
| 5 |
13 |
COBRA |
ESR1 |
gb|M69297.1| [BISUL_UNMETH_RC] |
46.1 (23) |
0.006 |
gb|AE014307.1| [BISUL_UNMETH_RC] |
40.1 (20) |
0.40 |
| 6 |
16 |
COBRA |
FLT1 |
emb|AL139005.12| [BISUL_UNMETH_RC] |
40.8 (20) |
0.22 |
emb|AL731546.4| [BISUL_UNMETH_FW] |
38.8 (19) |
0.91 |
| 7 |
24 |
BiSeq |
CDKN2C |
gb|AY094608.1| [BISUL_UNMETH_FW] |
50.1 (25) |
4e-04 |
gb|AC027334.5| [BISUL_UNMETH_FW] |
40.1 (20) |
0.43 |
| 8 |
83 |
BiSeq |
SERPINB5 |
gb|AC036176.8| [BISUL_UNMETH_RC] |
60.0 (30) |
7e-07 |
emb|AL133413.5| [BISUL_UNMETH_FW] |
52.0 (26) |
2e-04 |
| 9 |
1 |
MSP-unmeth |
VHL |
gb|AC018808.5| [BISUL_UNMETH_RC] |
48.1 (24) |
0.002 |
emb|AL513423.3| [BISUL_UNMETH_RC] |
44.1 (22) |
0.025 |
| 10 |
1 |
MSP-meth |
VHL |
gb|L15409.1| [BISUL_METH_FW] |
44.1 (22) |
0.021 |
gb|AC079148.9| [BISUL_METH_FW] |
36.2 (18) |
5.1 |
| 11 |
17 |
MSP-unmeth |
CDKN2A |
dbj|AB060808.1| [BISUL_UNMETH_RC] |
48.1 (24) |
0.002 |
emb|AL137127.7| [BISUL_UNMETH_RC] |
42.1 (21) |
0.11 |
| 12 |
17 |
MSP-meth |
CDKN2A |
gb|AF044170.1| [BISUL_METH_FW] |
48.1 (24) |
0.002 |
emb|AL137077.31| [BISUL_METH_RC] |
36.2 (18) |
6.4 |
| 13 |
Ref [15] |
MSP-unmeth |
CDKN2A |
dbj|AP001626.1| [BISUL_UNMETH_RC] |
38.2 (19) |
1.7 |
emb|AL161774.49| [BISUL_UNMETH_FW] |
44.1 (22) |
0.028 |
| 14 |
Ref [15] |
MSP-meth |
CDKN2A |
Na |
Na |
Na |
gb|AC092171.4| [BISUL_METH_FW] |
38.2 (19) |
1.7 |
|
This list summarizes the output of 14 individual methBLAST searches. We randomly selected two assays from the five assay types available in methPrimerDB and listed the sequence identifier, the score and E value of the best hit when both the forward and reverse primer align correctly on the desired target and of the first alignment on an undesired target sequence. The MSP assays have two primer pairs resulting in two methBLAST outputs (9–14). All misalignment hits are the result from partial alignment of one of the primers of an assay. This does not result in aspecific amplification. The alignments of the primers from the assays submitted in methPrimerDB are correct and do not demonstrate any potentially amplifiable misalignments. Alignment results #13 and #14 were generated with primers published in literature [15] that are almost identical to the primers from methPrimerDB ID 17 for which the results are numbered as #11 and #12. Result #13 shows correct but incomplete alignment compared to result #12 and attempt #14 does not lead to any correct alignment. Abbreviations: ID: methPrimerDB ID; BiPS: PCR-single-strand conformation polymorphism analysis; Ms-SNuPE: methylation-sensitive single-nucleotide primer extension; COBRA: combined bisulphite restriction analysis; BiSeq: Bisulphite Sequencing; MSP-unmeth: methylation-specific PCR for unmethylated target detection; MSP-meth: methylation-specific PCR for methylated target detection | |||||||||
Pattyn et al. BMC Bioinformatics 2006 7:496 doi:10.1186/1471-2105-7-496 |
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