Difference between revisions of "Task 5: Mapping point mutations"
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== Comparing the annotation of HGMD and SNPdb == |
== Comparing the annotation of HGMD and SNPdb == |
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=== Alignment of the reference sequences === |
=== Alignment of the reference sequences === |
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| + | We decided to use the sequence of PAH of Uniprot (see [http://www.uniprot.org/uniprot/P00439.txt UniProt]). |
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| + | * <code>MSTAVLENPGLGRKLSDFGQETSYIEDNCNQNGAISLIFSLKEEVGALAKVLRLFEENDV<br> |
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| + | NLTHIESRPSRLKKDEYEFFTHLDKRSLPALTNIIKILRHDIGATVHELSRDKKKDTVPW<br> |
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| + | FPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQFADIAYNYRHGQPIPRVEYM<br> |
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| + | EEEKKTWGTVFKTLKSLYKTHACYEYNHIFPLLEKYCGFHEDNIPQLEDVSQFLQTCTGF<br> |
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| + | RLRPVAGLLSSRDFLGGLAFRVFHCTQYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFA<br> |
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| + | QFSQEIGLASLGAPDEYIEKLATIYWFTVEFGLCKQGDSIKAYGAGLLSSFGELQYCLSE<br> |
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| + | KPKLLPLELEKTAIQNYTVTEFQPLYYVAESFNDAKEKVRNFAATIPRPFSVRYDPYTQR<br> |
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| + | IEVLDNTQQLKILADSINSEIGILCSALQKIK</code> |
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| + | |||
| + | ====Alignment with the reference sequence used in HGMD==== |
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| + | |||
| + | ====Alignment with the reference sequence used in SNPdb==== |
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=== Mapping === |
=== Mapping === |
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Revision as of 13:53, 15 June 2011
Contents
Task description
A detailed task description can be found here: Mapping point mutations
SNP databases
HGMD
- HGMD
- Searched for PAH
- 429 Missense/Nonsense mutations known by HGMD Professional
There are several mutation types known for PAH:
- Missense/nonsense
- Splicing
- Regulatory
- Small deletions
- Small insertions
- Small indels
- Gross deletions
- Gross insertions/duplications
- Complex rearrangements
One additional category of mutation is known, but is not recorded for PAH
- Repeat variations
Reference Sequence
The reference sequence is given by the accession number NM_000277.1, whose entry contains the following amino acid sequence:
MSTAVLENPGLGRKLSDFGQETSYIEDNCNQNGAISLIFSLKEEVGALAKVLRLFEEN DVNLTHIESRPSRLKKDEYEFFTHLDKRSLPALTNIIKILRHDI GATVHELSRDKKKDTVPWFPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQ FADIAYNYRHGQPIPRVEYMEEEKKTWGTVFKTLKSLYKTHACYEYNHIFPLLEKYCG FHEDNIPQLEDVSQFLQTCTGFRLRPVAGLLSSRDFLGGLAFRVFHCTQYIRHGSKPM YTPEPDICHELLGHVPLFSDRSFAQFSQEIGLASLGAPDEYIEKLATIYWFTVEFGLC KQGDSIKAYGAGLLSSFGELQYCLSEKPKLLPLELEKTAIQNYTVTEFQPLYYVAESF NDAKEKVRNFAATIPRPFSVRYDPYTQRIEVLDNTQQLKILADSINSEIGILCSALQK IK
SNPs
SNPdb
Reference Sequence
SNPs
Comparing the annotation of HGMD and SNPdb
Alignment of the reference sequences
We decided to use the sequence of PAH of Uniprot (see UniProt).
MSTAVLENPGLGRKLSDFGQETSYIEDNCNQNGAISLIFSLKEEVGALAKVLRLFEENDV
NLTHIESRPSRLKKDEYEFFTHLDKRSLPALTNIIKILRHDIGATVHELSRDKKKDTVPW
FPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQFADIAYNYRHGQPIPRVEYM
EEEKKTWGTVFKTLKSLYKTHACYEYNHIFPLLEKYCGFHEDNIPQLEDVSQFLQTCTGF
RLRPVAGLLSSRDFLGGLAFRVFHCTQYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFA
QFSQEIGLASLGAPDEYIEKLATIYWFTVEFGLCKQGDSIKAYGAGLLSSFGELQYCLSE
KPKLLPLELEKTAIQNYTVTEFQPLYYVAESFNDAKEKVRNFAATIPRPFSVRYDPYTQR
IEVLDNTQQLKILADSINSEIGILCSALQKIK
