# EPN, Tue Jun  8 13:27:18 2010
#
# README for the models/ subdirectory of SSU-ALIGN source distribution.
#
# This directory contains files related to the three default
# models used by SSU-ALIGN 0.1.  The models are based on alignments
# derived from the Comparative RNA Website (CRW; http://www.rna.ccbb.utexas.edu),
# and are redistributed here with permission from Robin Gutell (see 
# the email correspondence at the end of this file).
# 
# The following files exist 
# For each family <fam>, where <fam> is either "archaea", 
# "bacteria", or "eukarya"
# 
# <fam>-0p1.cm:   the CM file for the family
# <fam>-0p1.stk:  the seed alignment for the family
# <fam>-0p1.fa:   unaligned versions of the seed alignment sequences
# <fam>-0p1.mask: the default mask for the family
# <fam>-0p1.ps:   the postscript template file for the family
#                 used by ssu-draw.
#
# The following files contain info on all three families. They
# are simply the three per-family files concatenated together.
#
# ssu-align-0p1.cm:  All 3 default models.
# ssu-align-0p1.stk: All 3 default seed alignments
# ssu-align-0p1.ps:  All 3 default postscript template files.
# 
# rebuild-default-models.sh: contains the commands used to build the 
#                            default CMs from the default seeds.
#
##################################################
# Email from Robin Gutell concerning permission to redistribute
# alignments derived from CRW:
#
Dear Eric,

I just realized that I had not responded to your email from last
May, although I thought that I did respond last May!

Below is an email that I sent Elena last August (2007)

You will see that I had already agreed to let your group distribute
my lab's CRW Alignments - see my email to Elana.

I'm glad that my lab can contribute to our efforts.

Please let me know if this is adequate.

I sincerely apologize for the very (very) slow response.

With best wishes,
Robin
------------
Date: Fri, 17 Aug 2007 13:47:02 -0400 (EDT)
From: Elena Rivas <rivase@janelia.hhmi.org>
Subject: Re: your mail
To: Robin Gutell <robin.gutell@mail.utexas.edu>
Cc: Elena Rivas PhD <rivase@janelia.hhmi.org>

Hello Robin,

thank you for your response. It is great news. The CRW site
has been very useful, and not just for me. Other members of
the lab (Eric Nawrocki and Diana Kolbe) who are working on
new algorithms for Infernal, are also using or thinking of
using the CRW alignements.

> I'm pleased that data from the CRW Site is contributing to your
> research. You are most welcome to make your reformatted CRW
> alignments
> available with your supplementary data. Is it possible to include
> the
> CRW name and URL in the alignment file, so people would know the
> history of that alignment (and also include a statement about your
> modifications to this alignment). I want people to alert the CRW
> Site
> if any of these alignments have problems. Our goal is to improve the
> accuracy and utility of the CRW data.

It should be straightforward to add the name, url and reference to
the CRW Site into the Stockholm format to which we routinely convert the
alignments. I will make sure I do that before I submit the paper.

------------
Date: Thu, 16 Aug 2007 19:14:35 -0500
From: Robin Gutell <robin.gutell@mail.utexas.edu>
Subject: Re: your mail
To: Elena Rivas <rivase@janelia.hhmi.org>
Cc: Robin Gutell <robin.gutell@mail.utexas.edu>

Hello Elana,

I'm pleased that data from the CRW Site is contributing to your
research. You are most welcome to make your reformatted CRW alignments
available with your supplementary data. Is it possible to include the
CRW name and URL in the alignment file, so people would know the
history of that alignment (and also include a statement about your
modifications to this alignment). I want people to alert the CRW Site
if any of these alignments have problems. Our goal is to improve the
accuracy and utility of the CRW data.

Once your manuscript is available for distribution, I would be very
interested in receiving a copy.

I have been wondering if Sean's Rfam and my lab's CRW Project might
want to collaborate in some areas to enhance the amount, accuracy, and
detail of the RNA information we make available to the larger
scientific audience. Our efforts have been, in general, complementary.  We are
working on a new data infrastructure that will allow us to increase
the types of information at the CRW Site [e.g. RNAMap Secondary Structure
Java Applet and Crystal Structure information (both in section 2A),
and Structural Statistics (section 2D)]. These are the beginnings of a
larger effort (and hopefully we will receive more funding to bring
this effort to fruition).

If you and Sean are interested in discussing this Rfam/CRW issue, then
maybe we can arrange to meet when I'm on the east coast this upcoming
October to attend a meeting with my database collaborators.



With best wishes,
Robin

On Wed, Aug 15, 2007 at 10:58:05AM -0400, Elena Rivas wrote:
> Date: Wed, 15 Aug 2007 10:58:05 -0400 (EDT)
> From: Elena Rivas <rivase@janelia.hhmi.org>
> To: robin.gutell@mail.utexas.edu
>
>
> Dear Dr. Gutell,
>
> I am writing a manuscript that uses a reformatted subset of the SSU
> and LSU rRNA sequence alignments from the CRW Site to benchmark a new
> software application for phylogenetic inference. The source of the
> alignments is cited in my paper following the guidelines of the CRW
> Web Site.  I will also need to make my data files available as
> supplementary material for my paper, in order for my benchmarks to be
> reproducible.  Because this would amount to redistributing your data,
> in accordance with the data access policy expressed on the CRW Web
> site, may I have your written permission to release my reformatted
> data as supplemental material for my manuscript?
>
> Thanks for your attention,
> Elena Rivas
------------
On Fri, May 02, 2008 at 04:09:24PM -0400, Nawrocki, Eric P. wrote:
> Date: Fri, 2 May 2008 16:09:24 -0400
> From: "Nawrocki, Eric P." <nawrockie@janelia.hhmi.org>
> Subject: SSU alignments question from Janelia Farm
> To: robin.gutell@mail.utexas.edu
>
> Dr. Gutell,
>
> I hope everything is going well with you since your visit to Janelia
> Farm last October. This e-mail is long overdue. We had spoken while
> you were here at Janelia about using your SSU alignments to build
> covariance models with our Infernal software. I asked if it was okay
> with you if we distributed alignments based on your CRW alignments
> provided that we emphasize the origin of the alignments (your website)
> and stress that the website be cited if the alignments were useful for
> any publication. My memory is that you said it was okay under those
> terms. You had asked that I write you an e-mail that included this
> information. Unfortunately I was working on other projects and forgot
> to send the e-mail until now. I'm sorry it slipped my mind.
>
> The issue has come up again because we have been contacted about SSU
> alignment from a group at the Broad institute asking us if we have any
> good alignments for building SSU covariance models. I was planning on
> sending our SSU alignments which are based on your CRW alignments and
> stressing that if they lead to any publications they must cite your
> website as the source of the data.
>
> Please let me know how you feel about us distributing our SSU
> alignments that are based on your CRW SSU alignments.
>
> Thanks!
>
> Eric Nawrocki
> Ph.D. Student
> Eddy lab
> Janelia Farm Research Campus
> Howard Hughes Medical Institute

