Documentation for Advanced Data Retrieval Tool for SNPs v0.9

With Advanced Data Retrieval Tool for SNPs (ARTS) you a able to retrieve SNPs from the XML Files of the NCBI's dbSNP
that have a common genotype in two substrains of laboratory mice and a different one in a third.

This allows for the generation of a SNP marker panel that can be incorporated into a backcrossing scheme which can employ two
different outcross strains giving the researcher more flexibility in terms of dealing with loss of phenotys due to the genetic background of the outcross strain.

It is also possible to select more than one strain within every scrolling list. Therefore it is possible to select a whole
family of substrains within which you won't expect too many genetic variations
(like BALB/C, BALB/CJ, BALB/BCY, and BALB/CBYJ) to increase the number of hits.

Note that the boolean relation between the strains selected within one scrolling list can be seen as an OR and the boolean relation
between each scrolling list can be seen as an AND or NOT respectively.

Known Bugs and Workarounds

There is no check if the numbers entered into "region from" and "to" are correct, so make sure that you enter them correctly
If you activate "display monomorphic SNPs" and you are going to analyze a large region, be prepared to wait for a while

Short Term Outlook

Integration of dbSNP entries of other species like Rattus norvegicus or Danio rerio
Integration of human dbSNP data
Integration of an automapping function (see ARTS v1.0 alpha for a preview)
Export of selected SNPs in FASTA format

Long Term Outlook

Proof that ARTS can be used as a tool for retrieving haplotype patterns of mouse strains in silco
Proof that ARTS is capable of predicting common mutations in mouse strains (like the mutation in Tyrosinase in albino mouse strains (e.g. BALB/C, A)
Inter species comparison to find conserved SNPs among species