Table 2 Data sources

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