|
SNP rs or ss number*
|
User input
|
File or text input
|
1
|
|
Trivial name
|
User input
|
Same file as above
|
1
|
|
Size of assay sequence
|
User input
|
e.g. 200 specifies 200 nucleotides each side of assay SNP (401 altogether)
|
1
|
|
New rs number
|
NCBI dbSNP cluster page*
|
New rs retrieved when rs no longer in use** or if ss number submitted***
|
2
|
|
Fasta sequence, allele,
|
ditto
|
Fasta output with allele in header (major allele first)
|
2
|
|
Major allele, validation of assay, heterozygosity
|
ditto
|
'Allele' report.
| |
|
Fasta sequence (second attempt)
|
NCBI contig fasta sequence****
|
If sequence in cluster page too short: contig reference from cluster page*
|
2
|
|
Gene, chromosome
|
NCBI cluster page*
|
'Gene' report
|
2
|
|
Masked sequences
|
RepeatMasker (see text)
|
Takes fasta output above and produces fasta for next step.
|
3
|
|
Platform
|
User input
|
Choose TaqMan, SNPstream or Sequenom
|
3
|
|
Chromosome position, adjacent SNP list, with 21 nucleotide sequence etc.
|
Mysql local database with dbSNP data
|
Annotation of assay sequence using Seq4SNP algorithm
|
4
|
|
Validation, heterozygosity
|
Ditto
|
Part of Adjacent SNP Report (Fig 3) detailing each SNP and flagging placement mismatches
|
4
|
|
SNP assay sequences
| |
Final output compatible with assay designers
|
4
|
