Received: from localhost ([::1]:53932 helo=stodi.digitalkingdom.org) by stodi.digitalkingdom.org with esmtp (Exim 4.76) (envelope-from ) id 1TxLzA-0005OM-MD; Mon, 21 Jan 2013 10:20:45 -0800 Received: from mail-vc0-f181.google.com ([209.85.220.181]:64308) by stodi.digitalkingdom.org with esmtps (TLSv1:RC4-SHA:128) (Exim 4.76) (envelope-from ) id 1TxLyv-0005OH-G3 for jbovlaste@lojban.org; Mon, 21 Jan 2013 10:20:41 -0800 Received: by mail-vc0-f181.google.com with SMTP id d16so3579930vcd.26 for ; Mon, 21 Jan 2013 10:20:23 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:x-received:in-reply-to:references:date:message-id :subject:from:to:content-type; bh=qyRvpqID+kfuUVRtrrCvdpnmkfdgZy7DgaXmGhyxLLo=; b=alftqoC74t6hxbznJDhtGA4jwPMaU6TagiE1uiBpQWsOeDOMq21Gvp4Uykba4QZ5I0 P5OXeyQJr7/qorn/f2lOwnT5IEOPgCmFhUzw92mWLZQVvHBNFlrdGzMofHaZ7Tk3yIy/ ecbOzxvhO9gcJUX6fA+MCjNeeKhzeaSVDASVbwI0c/V+PPWqxS/L5nMVHVJehtUvGMYw aHAZqz3+hHtyG1hU7crlJRtp5RtsYnPm8Rklv42m+WbZm8zrsuO/X1A/I87EES8nqe1O ibqzHvn4krVdtxTVv/7Ep0u8Pp9dp1S8Wz6PhS3LwEcJaIkr3/+SZhmD4h+aWwEscpFu Ug2g== MIME-Version: 1.0 X-Received: by 10.52.19.241 with SMTP id i17mr18009464vde.67.1358792422878; Mon, 21 Jan 2013 10:20:22 -0800 (PST) Received: by 10.58.246.72 with HTTP; Mon, 21 Jan 2013 10:20:22 -0800 (PST) In-Reply-To: <1383085.hAMHNW2WL5@caracal> References: <3185684.p7HcNfvyA7@caracal> <1383085.hAMHNW2WL5@caracal> Date: Mon, 21 Jan 2013 13:20:22 -0500 Message-ID: From: Austin Thomas To: jbovlaste@lojban.org X-Spam-Score: 1.6 (+) X-Spam_score: 1.6 X-Spam_score_int: 16 X-Spam_bar: + X-Spam-Report: Spam detection software, running on the system "stodi.digitalkingdom.org", has identified this incoming email as possible spam. The original message has been attached to this so you can view it (if it isn't spam) or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: I think your definition of a RFLP is a bit off. It is just a restriction fragment and depending on the restriction enzyme or enzymes used the fragment lengths vary. Restriction sites can vary based on differing sequences therefore homologous regions can yield different fragment lengths. These can be statistically associated with particular alleles of genes and therefore associated with with particular phenotypes (diseases) but it actually doesn't have a direct link to it. The lengths do not differ (necessarily) between alleles in a RFLP, only the restriction sites (and these could stretch across multiple genes or be within a single allele). (I have done RFLP analysis so I hope I know what I am talking about) [...] Content analysis details: (1.6 points, 5.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- 0.0 FREEMAIL_FROM Sender email is commonly abused enduser mail provider (amt2839[at]gmail.com) 0.0 DKIM_ADSP_CUSTOM_MED No valid author signature, adsp_override is CUSTOM_MED -0.0 SPF_PASS SPF: sender matches SPF record 0.2 FREEMAIL_ENVFROM_END_DIGIT Envelope-from freemail username ends in digit (amt2839[at]gmail.com) 0.0 HTML_MESSAGE BODY: HTML included in message 0.1 DKIM_SIGNED Message has a DKIM or DK signature, not necessarily valid 0.0 T_DKIM_INVALID DKIM-Signature header exists but is not valid 1.2 NML_ADSP_CUSTOM_MED ADSP custom_med hit, and not from a mailing list Subject: Re: [jbovlaste] SNP, RFLP, allele X-BeenThere: jbovlaste@lojban.org X-Mailman-Version: 2.1.14 Precedence: list Reply-To: jbovlaste@lojban.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Content-Type: multipart/mixed; boundary="===============3134376572497254120==" Errors-To: jbovlaste-bounces@lojban.org --===============3134376572497254120== Content-Type: multipart/alternative; boundary=20cf30780bdab06eeb04d3d08373 --20cf30780bdab06eeb04d3d08373 Content-Type: text/plain; charset=ISO-8859-1 I think your definition of a RFLP is a bit off. It is just a restriction fragment and depending on the restriction enzyme or enzymes used the fragment lengths vary. Restriction sites can vary based on differing sequences therefore homologous regions can yield different fragment lengths. These can be statistically associated with particular alleles of genes and therefore associated with with particular phenotypes (diseases) but it actually doesn't have a direct link to it. The lengths do not differ (necessarily) between alleles in a RFLP, only the restriction sites (and these could stretch across multiple genes or be within a single allele). (I have done RFLP analysis so I hope I know what I am talking about) You also keep using allele improperly. An SNP is not an allele, it might possibly define an allele but allele does not refer specifically to single base pairs, at least not in any context that I am aware of. An allele can be non-coding though like is usually the case with VNTRs in which diffirent repeats are reffered to as different alleles. When talking about a coding sequence Allele refers to the entire protein encoding sequence. Allele is often used to refer to multiple protein encoding genes that all effect one phenotype although I am not sure that all molecular geneticists would agree with that usage but traditionally it was accepted. Personally I think ginpanra could work but note that these are homologues not identical strands, alleles are different sequences. On Mon, Jan 21, 2013 at 12:03 AM, Pierre Abbat wrote: > On Sunday, January 20, 2013 21:33:36 Eitan Postavsky wrote: > > SNP: If you don't mind my suggesting an entirely different veljvo, I > think > > the key word is {panra}. An SNP is a terpanra be lo jgina bei lo jgina, > > y'see? > > So is a RFLP, if I understand you right. And neither has to be in a gene. > > > RFLP: Are you referring to the difference between homologous DNA > molecules > > or the laboratory technique? Oh well, I don't understand either. > > I'm referring to a site on a chromosome where different alleles differ in > the > distance between consecutive occurrences of some sequence. It could be a > variable-length repetition; it could be a SNP where one of the alleles is > in > the sequence. > > > Allele: ginpanra. It's two jgina that panra each other, not differing in > > their terjgina. I'm aware that you're thinking of an allele as a > particular > > sequence of base pairs that implements a given terjgina, but ginpanra > works > > too, doesn't it? > > Let's take a concrete example: OPN1LW. I was looking that up because I have > some mutation of it. OPN1LW codes for the protein which combines with > something to make it see red. It has seven SNPs (one is listed as > "deleted"), > each of which may cause some change to the protein. There are three > phenotypes > in men and four in women (it's on X): normal red vision, tetrachromacy > (only > in women), protanopia, and protanomalopia. There are three alleles > distinguishable without looking at the SNPs: normal, missense causing > protanomalopia, and nonsense causing protanopia. I can't tell which SNP is > which from SNPedia, because it says "protan", and I don't know whether it > means protanopia, protanomalopia, or both. > > la'o .gin. OPN1LW .gin. jgina lo remna lo jei je ka viska lo xunre > > Let's denote the three alleles by R, R', and r. I'd like to say: > > la'o zoi. R' .zoi la'o .gin. OPN1LW lo ka frica viska lo xunre > > or with x2 and x3 exchanged. > > Pierre > -- > gau do li'i co'e kei do > > > _______________________________________________ > jbovlaste mailing list > jbovlaste@lojban.org > http://mail.lojban.org/mailman/listinfo/jbovlaste > --20cf30780bdab06eeb04d3d08373 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I think your definition of a RFLP is a bit off. =A0It is just a restriction= fragment and depending on the restriction enzyme or enzymes used the fragm= ent lengths vary. =A0Restriction sites can vary based on=A0differing=A0sequ= ences therefore homologous regions can yield different fragment lengths. Th= ese can be statistically associated with particular alleles of genes and th= erefore associated with with particular phenotypes (diseases) but it actual= ly doesn't have a direct link to it. =A0The=A0lengths=A0do not differ (= necessarily) between alleles in a RFLP, only the restriction sites (and the= se could stretch across multiple genes or be within a single allele). (I ha= ve done RFLP analysis so I hope I know what I am talking about)

You also keep using allele improperly. =A0An SNP is not an a= llele, it might possibly define an allele but allele does not refer specifi= cally to single base pairs, at least not in any context that I am aware of.= =A0An allele can be non-coding though like is usually the case with VNTRs = in which diffirent repeats are reffered to as different alleles. =A0When ta= lking about a coding sequence Allele refers to the entire protein encoding = sequence. =A0Allele is often used to refer to multiple=A0protein=A0encoding= genes that all effect one phenotype although I am not sure that all molecu= lar geneticists would agree with that usage but=A0traditionally=A0it was ac= cepted.

Personally I think ginpanra could work but note that th= ese are homologues not identical strands, alleles are different sequences.<= /div>

On Mon, Jan 21, 2013 at 12:03 AM, = Pierre Abbat <phma@bezitopo.org> wrote:
On Sunday, January 20, 201= 3 21:33:36 Eitan Postavsky wrote:
> SNP: If you don't mind my suggesting an entirely different veljvo,= I think
> the key word is {panra}. An SNP is a terpanra be lo jgina bei lo jgina= ,
> y'see?

So is a RFLP, if I understand you right. And neither has to be in a g= ene.

> RFLP: Are you referring to the difference between homologous DNA molec= ules
> or the laboratory technique? Oh well, I don't understand either.
I'm referring to a site on a chromosome where different alleles d= iffer in the
distance between consecutive occurrences of some sequence. It could be a variable-length repetition; it could be a SNP where one of the alleles is i= n
the sequence.

> Allele: ginpanra. It's two jgina that panra each other, not differ= ing in
> their terjgina. I'm aware that you're thinking of an allele as= a particular
> sequence of base pairs that implements a given terjgina, but ginpanra = works
> too, doesn't it?

Let's take a concrete example: OPN1LW. I was looking that up beca= use I have
some mutation of it. OPN1LW codes for the protein which combines with
something to make it see red. It has seven SNPs (one is listed as "del= eted"),
each of which may cause some change to the protein. There are three phenoty= pes
in men and four in women (it's on X): normal red vision, tetrachromacy = (only
in women), protanopia, and protanomalopia. There are three alleles
distinguishable without looking at the SNPs: normal, missense causing
protanomalopia, and nonsense causing protanopia. I can't tell which SNP= is
which from SNPedia, because it says "protan", and I don't kno= w whether it
means protanopia, protanomalopia, or both.

la'o .gin. OPN1LW .gin. jgina lo remna lo jei je ka viska lo xunre

Let's denote the three alleles by R, R', and r. I'd like to say= :

la'o zoi. R' .zoi <allele> la'o .gin. OPN1LW lo ka frica = viska lo xunre

or with x2 and x3 exchanged.

Pierre
--
gau do li'i co'e kei do


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