[Bio-software] Re: Bio-soft Digest, Vol 37, Issue 7

[Francis Ouellette]

It took some digging (and asking at blast-help from ncbi.nlm.nih.gov),
but here is what I got:

>     It's listed among the amino acids at
> http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/BIOSEQ.HTML

J is "Leu or Ile"

(from IUPAC and NCBI)

Other "specials" are:

B    Asp or Asn
J    Leu or Ile
O    Pyrrolysine
X    Undetermined or atypical
Z    Glu or Gln

O is not used in BLOSOM (currently).

Cheers,

f.


--
B.F. Francis Ouellette         http://oicr.on.ca/research/ouellette/
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________________________________
>From: Linlin Yan <yanlinlin82 from gmail.com>
Date: Fri, 27 Jun 2008 22:03:41 -0400
To: <bionet-software from net.bio.net>
Subject: [Bio-software] Re: Bio-soft Digest, Vol 37, Issue 7

On Jun 28, 1:52 am, "Harianto Tjong" <haria... from mailer.sb.fsu.edu>
wrote:
> I think J=W ( or Trp).
> For some purpose, amino acids are coded into the first 20 letters of
> alphabet, so after the 20th in alphabetical order  (T=Threonine), there are
> 3 amino acids need to be mapped to fit: V,W,Y into B,J,O (for Val, Trp,
> Tyr).

I'm afraid the map may be wrong. Usually B means Asp or Asn, but not
Val.
I haven't seen J or O letter before I found J in NCBI scoring matrix.
I guess Raoul Fleckman must be right: J means Leu or Ile. Need to be
reassured.

> Maybe others can correct me if I'm wrong.
>
> On Fri, Jun 27, 2008 at 1:03 PM, <bio-soft-requ... from oat.bio.indiana.edu>
> wrote:
>
>
>
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> >   1. Re: Which amino acid residue does the letter 'J'  mean?
> >      (Raoul Fleckman)
>
> > ----------------------------------------------------------------------
>
> > Message: 1
> > Date: Thu, 26 Jun 2008 17:34:55 -0500
> > From: Raoul Fleckman <raoul.fleck12... from comcast.com>
> > Subject: [Bio-software] Re: Which amino acid residue does the letter
> >        'J'     mean?
> > To: bionet-softw... from net.bio.net
> > Message-ID: <slrng686ch.94d.raoul.fleck... from comcast.com>
>
> > Leucine or Isoleucine
>
> > On 2008-06-25, Linlin Yan <yanlinli... from gmail.com> wrote:
> > > I just found there is a letter 'J' in NCBI's scoring matrix file
> > > (e.g. /usr/share/ncbi/data/BLOSUM50). Does anybody know what it is?
> > > Thanks!
>

> --
> Harianto Tjong
> 419 IMB
> Florida State University
> Tallahassee, FL 32306
> Tel : (850) 645-1334
> Fax : (850) 644-7244http://people.scs.fsu.edu/~harianto


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