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SNPedia talk:FAQ

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These 'questions' were posted to the article. I'm unable to answer them, and until someone else is I think they belong here on discussion. Cariaso 22:58, 24 August 2007 (CDT)

4.DETAIL Regarding repeats and Single nucleotide polymorphism ?

5.SNP detection methods:SSCP,PCR-based,dHPLC,sequencing?

6. SNP & disease?

Further information about genotype mismatches and strand choice[edit]

It might be useful to direct the user to one or more of the following web pages, for further information about the different standards of genotype notation on the different (test) platforms. Hope this helps. E:V:A 15:21, 4 October 2010 (UTC)

Excerpt from above:

Strand Specification:

Consider the case of a SNP (an A/T polymorphism colored red) shown below in double stranded sequence:

5'-GATTAGTA[A/T]GCCGAGCTG-3' --> Forward strand
3'-CTAATCAT[T/A]CGGCTCGAC-5' <-- Reverse strand

One submitter reports the frequency of the alleles observed with regard to the forward strand as: A = .25 and T= .75

A second submitter reports the frequency of the alleles observed on the reverse strand as: A = .75 and T=.25

Without strand information, these results would appear to contradict each other because an observer would make the assumption that both submitters were reporting allele frequencies with respect to the forward strand. When strand is taken into consideration, it is apparent to an observer that these two submitters are reporting equivalent allele frequencies.

Array extension request[edit]

How many SNPs are in SNPedia?[edit]

Please install the Array Extension With it I can use arraydiff to automatically generate a table of SNPs that are unique to a microarray.

Currently the "Ask" framework doesn't allow NOTs, so currently you can generate the total list, and the list of those in common, but you cannot generate a count of how many SNPs are only found in a specific microarray.

This data could then be used to determine which combinations of tests would get you the most complete SNP coverage. I would use arraydefine to generate each array once, then reuse those arrays to cut down on computation load.

Nothing (shows total) Microarray_A Microarray_B Microarray_C All_Microarrays_except_current_row
Unique to Microarray_A as compared to total 0 data data data
Unique to Microarray_B as compared to total data 0 data data
Unique to Microarray_C as compared to total data data 0 data

Test case to determine if Array Extension is functioning:



test_array_a = {{#arrayprint:test_array_a}}

test_array_b = {{#arrayprint:test_array_b}}

{{#arraydiff:only_in_test_array_a |test_array_a |test_array_b }}

{{#arraydiff:only_in_test_array_b |test_array_b |test_array_a }}

only_in_test_array_a = {{#arrayprint:only_in_test_array_a}} (should equal blue)

only_in_test_array_b = {{#arrayprint:only_in_test_array_b}} (should equal white)

it is now installed. --- cariaso 00:47, 8 December 2013 (UTC)