Seq4SNPs tour

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Seq4SNPs tour

• One SNP, then file of SNPs

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One SNP (checklist)

• Type in SNP name (optional) and rs (required)
• (optional) change sequence assay size from 200
• Click Go
• Now you have fasta
• Optional save fasta for Repeat masking
• Click Add adjacent SNPs to fasta or masked
  sequence
• Go to next page
• Optional add Repeat masked file
• Choose assay format (ABI, SNPstream, iPLEX
• Click Add adjacent SNPs
• Finally save your output sequence file
• Check adjacent SNP report IF flagged
• All SNP placement by sequence matching

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RS
NAME (optional)
Sequence size (401)
GO
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1. Click here for your Fasta file
(save it for RepeatMasker)
OR click this to continue
OR click this to continue
(miss 3 slides)
2. Link to Repeat Masker with instructions
Link to BLAST with instructions
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You clicked through to the fasta file created by
Seq4SNPs
Use File gt Save as to save this
file Then go Back Use the link to Repeat
Masker and use this file in it
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In Repeat MaskerClick through to the masked file

File gt Save as to keep a file, or copy the
text Make a simple FILENAME (dont use the
default as there are too many stops)
Now return to Seq4SNPs
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NOW click this to continue

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1. (optional) If repeat masking, browse for your
file or paste in the text Also, uncheck box above
2. Choose file format
3. GO
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Formatted output file
Adjacent SNP report
Sequence displayed for a single SNP
Links to dbSNP
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You forgot where you were and now have the
repeat masked file
Use this link http//www.srl.cam.ac.uk/cgi-bin/on
cology/srl/ncbi/seq4snp3.pl
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(If asked, Supply the original Fasta file)
Masked file (with simple name)
Choose format and GO
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Now for a file of SNPs

• Add file
• (optional) change sequence assay size from 200
• Click Go
• Next page.. Click continue
• Now you have fasta
• Optional save fasta for Repeat masking
• Go to next page Click Add adjacent SNPs
• Optional add Repeat masked file
• Choose assay format (ABI, SNPstream, iPLEX
• Press Go
• Next page.. Click continue
• Finally save your output sequence file
• Check adjacent SNP report IF flagged
• All SNP placement by sequence matching
• NB. For large numbers of SNPs, if process stops
  partway through, you will have LINKS to the
  output files and can monitor progress.

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