RootsWeb: GENEALOGY-DNA-L Re: Ymatch query grammar

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Archiver > GENEALOGY-DNA > 2006-01 > 1136131642

From: Thomas Krahn <>
Subject: Re: Ymatch query grammar
Date: Sun, 01 Jan 2006 17:07:22 +0100
References: <003601c60e52$92cb1e10$0300a8c0@Seymour>
In-Reply-To: <003601c60e52$92cb1e10$0300a8c0@Seymour>

Dear Henry, I am answering this to you and the Genealogy-DNA list, because I think it is of general interest: Henry Seymour asked: > I am not a registered member of your site but I assumed that I could > access the database like I do on other sites. I entered my values and > clicked on the Search button but nothing happened. The Ymatch database has still too few entries, so it is quite unlikely that anybody will match your profile on all markers (except if your own entry is in the database). Start with entering 2 or 3 markers from your profile and you will get several hits. With this principle you can filter related haplotypes of any degree. It makes sense to start with markers with a low mutation frequency and then proceed to the markers with a higher mutation rate. This way it is possible to find geographical clusters or filter for markers that are typical for certain haplogroups or subhaplogroups. It is also possible to save a static link to a certain query: The basic link to Ymatch is http://www.dna-fingerprint.com/modules.php?op=modload&name=ymatch Now you can add search parameters to this link by simply adding "&Marker=Value". For example "&DYS390=23&DYS391=10&DYS392=11&DYS393=12" would filter out all haplotypes that have DYS390 23 and DYS391 10 and DYS392 1 1 and DYS393 12 Complete link: http://www.dna-fingerprint.com/modules.php?op=modload&name=ymatch&DYS390=23&DYS391=10&DYS392=11&DYS393=12 Or: *http://tinyurl.com/agftt * A quite typical signature for haplogroup J, isn't it? You should urgently have in mind, that Ymatch uses the ISFG & NIST nomenclature for the entries! [1] So if you have been tested by FTDNA, you must add +1 unit to your Y-GATA-H4 allele to match the correct nomenclature. Also, if you have your results for DYS463 from Relative Genetics or from DNA Heritage you must add 2 units. All conversions can be found on our YSTR nomenclature conversion table: http://www.dna-fingerprint.com/modules.php?op=modload&name=Sections&file=index&req=viewarticle&artid=12 > You don't provide instructions on how to enter multiple values for > markers such as 459a and 459b, and 464a-d. i.e. commas, semicolons, etc. > What are those for funny markers, that you mention there? You probably mean DYS459 and DYS464. The DYS in the signature is important, so you can't leave it away. Example: DYS385 is a completely different marker than DYF385. Also the a, b, c ... suffix is completely wrong in this context! The standardized nomenclature doesn't use it, if the alleles aren't really separately typed. See [1]: http://www.cstl.nist.gov/div831/strbase/pub_pres/ISFG_%20Y-STRupdate.pdf The misleading a, b, c .. signature makes the impression that it wasn't posible that the "a" allele can also match the "c" allele of the DYS464 marker. The only duplicated marker until today that can be typed with separate alleles is DYS385. Only in this special case you can use DYS385a* and DYS385b* and only if the alleles are really typed separately with the method of Kittler et al [2]. The correct nomenclature to list the alleles of multicopy markers is to write the alleles with dashes: Example: DYS459 9-10 DYS464 13-14-17-17 This is the way you are supposed to use if you make a query with Ymatch. If you type in 9-10 in the DYS459 field, you will get all results having 9 AND 10 at the DYS459 marker. You will get the same result, if you type in 10-9 , because the order of the alleles isn't specified. If you type in 9 only, you will get hits with all entries that contain at least one allele with 9 repeats. Examples: 9-10, 9-9, 8-9 or 9 (with a deletion). If you explicitely want to search for 9-9 alleles, you must type in 9-9 and you will leave out all other mixed alleles. The same is for DYS464: Examples: 14-14-17-17 will find all entries with exacly this haplotype, but also an unusual 14-14-17-17-18 entry with 5 alleles. 14-17 will find all haplotypes containing 14 and 17. Like: 14-14-17-17, 14-15-17-17, 14-15-17-18, also 14-17 (with an AZFc deletion). This query method makes it much easier to find recLOH events in a large number of haplotypes. Some people have incomplete DYS464 alleles. For example 15.3 . You can use incomplete alleles with Ymatch to filter them, because they represent a very distinctive marker. DYS464 and DYF371 have also the possibility to allow queries with extended type allele calls. Examples: 15c in the DYS464 input field will filter all entries containing a C-type allele with 15 repeats. All of the hits will belong to haplogroup R1b. 12t in the DYF371 input field will filter all results that have DYS425 = 12 The input field for the haplogroups is organized from the stem to the branches of the Y tree. A search for R1 will find all R1a and R1b haplogroups and varieties. The input field for the YSNP markers will also find any matching SNP in arbitary order. Every entry MUST have either a + or a - directly before the semicolon and directly after the marker name to be recognized by the search engine. Examples: P25+ will find all entries tested positive (derived) at P25. SRY2627- will find all entries tested negative (ancestral) for SRY2627 If you only want to search for datasets that are tested for a certain marker, you can use # as a replacement for + OR -. S21# will find all entries that have been tested for S21, regardless if the result was ancestral or derived. It isn't very useful to make enries like "M35C+" or "others-", because they will not be found, if the user will search for "M35+" or "M167-". I will try to implement a converter that automatically transfers the base notation to + or - and vice versa, as time permits, but at the moment I would recomend to use the +/- notation only, because this is the easiest way to handle it in the database for now. I wish all the best for 2006 to all, and I encourage everybody to enter their haplotypes in Ymatch to let the database grow! Never hesitate to ask questions! Thomas [1] L. Gusmao, J.M. Butler, A. Carracedo, P. Gill, M. Kayser, W.R. Mayr, N. Morling, M. Prinz, L. Roewer, C. Tyler-Smith , P.M. Schneider , "DNA Commission of the International Society of Forensic Genetics (ISFG): An update of the recommendations on the use of Y-STRs in forensic analysis" (2005) Forensic Science International, In Press, Corrected Proof, Available online 23 May 2005 http://www.cstl.nist.gov/div831/strbase/pub_pres/ISFG_%20Y-STRupdate.pdf [2] R. Kittler, A. Erler, S. Brauer, M. Stoneking and M. Kayser: "Apparent intrachromosomal exchange on the human Y chromosome explained by population history"; European Journal of Human Genetics (2003) 11, 304 – 314 http://www.eva.mpg.de/genetics/pdf/Kittler_EJHG_2003.pdf -- DNA-Fingerprint Tel.: +49-3329/697464 Fasanenstrasse 25a http://www.dna-fingerprint.com 14532 Stahnsdorf / Germany mailto:

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Re: Ymatch query grammar by Thomas Krahn <>