stash analysis logfile data for histogram construction

[sgn.git] / cgi-bin / solanaceae-project / sol-bioinformatics / ghent2006_report.pl

use strict;
use CXGN::Page;

my $page = CXGN::Page->new('Ghent 2006 Meeting Report','Robert Buels');
$page->add_style(text => '@page { size: 8.5in 11in; margin: 0.79in }\n' . <<EOS);
p { margin-bottom: 0.08in }
h1 { margin-bottom: 0.08in }
h1.western { font-family: "Arial", sans-serif; font-size: 16pt }
h1.cjk { font-family: "MS Mincho"; font-size: 16pt }
h1.ctl { font-family: "Tahoma"; font-size: 16pt }
h2 { margin-bottom: 0.08in }
h2.western { font-family: "Arial", sans-serif; font-size: 14pt; font-style: italic }
h2.cjk { font-family: "MS Mincho"; font-size: 14pt; font-style: italic }
h2.ctl { font-family: "Tahoma"; font-size: 14pt; font-style: italic }
h3 { margin-bottom: 0.08in }
h3.western { font-family: "Arial", sans-serif }
h3.cjk { font-family: "MS Mincho" }
h3.ctl { font-family: "Tahoma" }
EOS
$page->header();

print <<EOHTML;
<h1 class="western">Meeting Report: Tomato Annotation Meeting</h1>
<h2 class="western">Ghent, Belgium October 23-25<sup>th</sup>, 2006</h2>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">In Attendance</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in"><i>Belgium</i>:</p>
<ul>
        <li><p style="margin-bottom: 0in">St&eacute;phane Rombauts</p></li>
        <li><p style="margin-bottom: 0in">Pierre Rouz&eacute;</p></li>
        <li><p style="margin-bottom: 0in">Yves van der Peer (off and on)</p></li>
</ul>
<p style="margin-bottom: 0in"><i>Netherlands</i>:</p>
<ul>
        <li><p style="margin-bottom: 0in">Erwin Datema</p></li>
</ul>
<ul>
        <li><p style="margin-bottom: 0in">Mark Fiers</p></li>
        <li><p style="margin-bottom: 0in">Roeland van Hamm</p></li>
</ul>
<p style="margin-bottom: 0in"><i>India</i>:</p>
<ul>
        <li><p style="margin-bottom: 0in">Saloni Mathur</p></li>
        <li><p style="margin-bottom: 0in">Saurabh Raghuvanshi</p></li>
</ul>
<p style="margin-bottom: 0in"><i>Korea</i>:</p>
<ul>
        <li><p style="margin-bottom: 0in">Kyoo-Yeol Lee</p></li>
</ul>
<p style="margin-bottom: 0in"><i>Spain</i>:</p>
<ul>
        <li><p style="margin-bottom: 0in">Francisco Camara</p></li>
        <li><p style="margin-bottom: 0in">Roderic Guigo</p></li>
</ul>
<p style="margin-bottom: 0in"><i>France</i>:</p>
<ul>
        <li><p style="margin-bottom: 0in">Thomas Schiex</p></li>
</ul>
<p style="margin-bottom: 0in"><i>USA</i>:</p>
<ul>
        <li><p style="margin-bottom: 0in">Robert Buels</p></li>
        <li><p style="margin-bottom: 0in">Lukas Mueller</p></li>
</ul>
<p style="margin-bottom: 0in"><i>Italy</i>:</p>
<ul>
        <li><p style="margin-bottom: 0in">Maria Luisa Chiusano</p></li>
        <li><p style="margin-bottom: 0in">Alessandra Traini</p></li>
</ul>
<p style="margin-bottom: 0in"><i>Germany</i>:</p>
<ul>
        <li><p style="margin-bottom: 0in">Heiko Schoof (day 2)</p></li>
        <li><p style="margin-bottom: 0in">Anika Joecker</p></li>
</ul>
<p style="margin-bottom: 0in"><br /></p>
<h3 class="western">Purpose</h3>
<p style="margin-bottom: 0in">The purpose of the meeting was to
discuss the quality of a previously generated gene finder training
data set, discuss the performance of already trained, tomato specific
gene finders, define a distributed annotation pipeline for the tomato
genome sequences that are currently being generated, and to review
the data submission procedures. Representatives from 9 countries
involved in tomato sequencing and tomato annotation (through the
EU-SOL project) were attending the meeting.</p>
<p style="margin-bottom: 0in"><br /></p>
<h3 class="western">Day 1 &ndash; October 23, 2006</h3>
<p style="margin-bottom: 0in">First, a representative of every
country present gave a brief overview of the sequencing progress.</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">India discussed how overlapping
sequences were generated by sequencing seed BACs as far apart as 6cm.
Thus, the seed BACs need to be carefully analyzed for potential
overlaps, using the FPC fingerprint data. However, the FPC data is
not available for all BACs.</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">Mark Fiers and Erwin Datema reported on
trials with 454 sequences of full BACs. The feasibility of such an
approach is presently not clear. They also presented a demonstration
of Cyrille2, an interactive annotation pipeline system developed in
the Netherlands developed at their site.</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">Maria Luisa Chuisano gave an overview
of the EST alignment work and associated web resources that has been
developed in her lab at University of Naples.</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">Daniel Buchan gave a brief overview of
the state of chromosome 4 sequencing. Most of the BACs should be
available in early 2007.</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">Thomas, although himself not directly
involved on the sequencing side of things, presented progress on the
sequencing of the French project and mentioned a technology called
DAC, which allows many unfinished BACs to be finished in parallel. 
The technology is being actively developed. He also mentioned that
enough resources may be available to also sequence the
heterochromatic partion of chromosome 7. He then gave a brief
overview of Eugene.</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">Francisco presented an overview of
GeneID and a first tomato-specific matrix that was developed.</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">Next, Remy presented an analysis of the
training set that was manually generated by some members of the
group.  A total of 108 BACs were hand-annotated for complete and
clean gene models. However, the resulting dataset was not homogeneous
in quality, and some low-quality and/or incomplete gene models were
retained.  A discussion followed, in which St&eacute;phane Rombauts
explained that the poplar annotation project had used a very rigorous
automated method to generate a training set, and he suggested that we
try the same, letting the automated set supersede the hand-annotated
set.  A general agreement was reached to try this course, with the
automated generation performed by St&eacute;phane, using the same
methods from poplar.  St&eacute;phane also agreed to perform a trial
run of his training set generator during the meeting for evaluation.</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">The cornerstone of the training set
generation method is identifying annotations that are very
well-supported by EST alignments, and that match at least 75% of
their entire predicted protein to a known protein from Arabidopsis. 
With the number of sequenced BACs available, the trial run of his
training set generator produced only 100 very confident gene models
with the required level of EST support and Arabidopsis homology.  The
general conclusion was that this number was too low, but that the
method was quite promising, and that final evaluation of the method
should be deferred until more finished sequence is available.</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">The next discussion focused on the
submission process of the BAC sequences and annotations.  Currently,
all project partners are supposed to submit to Genbank and SGN
independently, which can lead to inconsistencies between the
repositories when the two submission events are far-separated in
time.  Daniel and Remy suggested submission to Genbank only, from
which SGN could pull in the sequences to feed into the annotation
pipelines. However, the problem with this approach is that under it,
the actual assembly data would not be carried by SGN.  A number of
attendees asserted that this assembly data is valuable for final
assembly and should continue to be rigorously warehoused.  Genbank
accepts the full BAC sequence and the chromatograms for the
individual sequence reads, but not the actual assembly data.  After a
long discussion, agreement was reached on the following protocol:
First, the finished BAC sequence must be submitted to Genbank, and a
Genbank accession obtained. Then, the sequences, including the
chromatograms and assembly information, is submitted to SGN, using
essentially the same submission format as now, but with an additional
file specifying the Genbank accession of the submission. SGN will
determine the Genbank accessions of the currently submitted sequences
and update them accordingly on the SGN FTP site.  In addition, the
following tags should be embedded in the comments field of each
submission to Genbank: &ldquo;ITAG&rdquo; (for International Tomato
Annotation Group) and &ldquo;TOMGEN&rdquo; (for Tomato Genome
Sequencing Project). This will allow to download all BACs that were
sequenced (TOMGEN) or annotated (ITAG) by searching Genbank for these
keywords. A quick search of Genbank determined that these keywords
are not presently in use by any other sequences.</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">In addition, Mark and Erwin at
Wacheningen will set up a central wiki site for use by the annotation
project for documenting the stages and interchange formats required
by the pipeline. (<b>update:</b><span style="font-weight: medium">
the wiki is up at <a href="http://www.ab.wur.nl/TomatoWiki">http://www.ab.wur.nl/TomatoWiki</a>
)</span></p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">A discussion on data formats concluded
that for most things, GFF3 should be sufficient. GAME XML is richer,
but is not as well-specified, and is the native format of Apollo. 
Artemis is also a very viable gene editor program, and it is capable
of using GFF3 as a native save format.  It was agreed that, for the
present at least, both GFF3 and GAME XML formats will be used, since
fairly well-developed conversion scripts exist at several of the
sites involved.</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in"><br /></p>
<h3 class="western">Day 2 &ndash; October 24, 2006</h3>
<p style="margin-bottom: 0in">The main focus of day 2 was
establishing a high-level design of the ITAG annotation pipeline. An
important aspect of the pipeline is that it is distributed, with many
annotation centers participating in the process, with each site doing
what they know to do best.  The pipeline is based on BAC sequences,
and whole pseudomolecule assemblies will also be run once they are
available (in a format to be determined later by the ITAG and TOMGEN
groups).</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">In summary, the complete pipeline is as
follows:</p>
<p style="margin-bottom: 0in"><br /></p>
<ol>
        <li><p style="margin-bottom: 0in">BAC sequences are uploaded to
        Genbank, and a genbank accession is obtained.</p></li>
        <li><p style="margin-bottom: 0in">The BAC is uploaded to SGN. 
        </p></li>
        <li><p style="margin-bottom: 0in">SGN runs vector screens and
        contamination screens (chloroplast, mitochondrial and human
        sequences), and does other quality control, such as comparison of <i>in
        vitro</i> (from FPC data) vs <i>in silico</i> restriction fragment
        sizes. The actual submission to Genbank will also be quality
        checked, sequences compared and the presence of the keywords (ITAG
        and TOMGEN) assured.</p></li>
        <li><p style="margin-bottom: 0in">SGN runs RepeatMasker with
        tomato-derived and other repeat databases.  This comes before the
        other pipeline steps so that some of them have the option of using
        the repeat-masked BAC sequence.</p></li>
        <li><p style="margin-bottom: 0in">in parallel:</p>
        <ul>
                <li><p style="margin-bottom: 0in">TBLASTX versus mimulus and potato
                sequences</p></li>
                <li><p style="margin-bottom: 0in">BLASTF (script from WUR) versus
                protein data sets</p>
                <ul>
                        <li><p style="margin-bottom: 0in">arabidopsis, swissprot,
                        solanaceae combined &ndash; SGN/Korea</p></li>
                        <li><p style="margin-bottom: 0in">other plants (rice, maize,
                        medicago, poplar) &ndash; PSB</p></li>
                        <li><p style="margin-bottom: 0in">swissprot</p></li>
                        <li><p style="margin-bottom: 0in">uniprot</p></li>
                        <li><p style="margin-bottom: 0in">pfam-B</p></li>
                        <li><p style="margin-bottom: 0in">SPTG</p></li>
                        <li><p style="margin-bottom: 0in">solanaceae</p></li>
                </ul>
                </li>
                <li><p style="margin-bottom: 0in">BLASTN</p>
                <ul>
                        <li><p style="margin-bottom: 0in">vector</p></li>
                        <li><p style="margin-bottom: 0in">e. coli</p></li>
                        <li><p style="margin-bottom: 0in">chloroplast</p></li>
                        <li><p style="margin-bottom: 0in">mitochondria (when available)</p></li>
                        <li><p style="margin-bottom: 0in">h. sapien</p></li>
                </ul>
                </li>
                <li><p style="margin-bottom: 0in">transcript sequence alignments
                (CAB Napoli)</p>
                <ul>
                        <li><p style="margin-bottom: 0in">tomato - 98% identity, 90%
                        coverage</p></li>
                        <li><p style="margin-bottom: 0in">solanaceae &ndash; 90% identity,
                        75% coverage</p></li>
                </ul>
                </li>
                <li><p style="margin-bottom: 0in">ab-initio gene finders</p>
                <ul>
                        <li><p style="margin-bottom: 0in">fgenesh (SGN)</p></li>
                        <li><p style="margin-bottom: 0in">genemark (remy)</p></li>
                        <li><p style="margin-bottom: 0in">glimmerhmm (erwin)</p></li>
                        <li><p style="margin-bottom: 0in">genscan - ? 
                        </p></li>
                        <li><p style="margin-bottom: 0in">genemark - ?</p></li>
                        <li><p style="margin-bottom: 0in">geneid (francisco/SGN)</p></li>
                        <li><p style="margin-bottom: 0in">SNAP (erwin</p></li>
                </ul>
                </li>
                <li><p style="margin-bottom: 0in">RFAM &ndash; blastn/infernal(?)</p></li>
                <li><p style="margin-bottom: 0in">tRNAscan-SE (SGN)</p></li>
        </ul>
        </li>
</ol>
<ul>
        <li>
        <ul>
                <li><p style="margin-bottom: 0in"></p></li>
        </ul>
        </li>
</ul>
<ol start="6">
        <li><p style="margin-bottom: 0in">All predictions, alignments and
        BLASTs are downloaded by U. Ghent and fed into Eugene.</p></li>
        <li><p style="margin-bottom: 0in">proteins from the Eugene
        predictions are then functionally annotated with</p>
        <ul>
                <li><p style="margin-bottom: 0in">BLASTP vs. Arabidopsis and rice
                proteins, against SwissProt</p></li>
                <li><p style="margin-bottom: 0in">Interpro &ndash; Imperial</p></li>
                <li><p style="margin-bottom: 0in">GO &ndash; MPIZ?</p></li>
                <li><p style="margin-bottom: 0in">TargetP, signalP, etc. - SGN</p></li>
                <li><p style="margin-bottom: 0in">RPSblast (MPIZ)</p></li>
                <li><p style="margin-bottom: 0in">TmHMM &ndash; SGN</p></li>
                <li><p style="margin-bottom: 0in">SGN Genes DB &ndash; SGN</p></li>
        </ul>
        </li>
        <li><p style="margin-bottom: 0in">SGN produces downloadable files
        and publishes them on FTP</p>
        <ul>
                <li><p style="margin-bottom: 0in">protein sequences</p></li>
                <li><p style="margin-bottom: 0in">cds/cdna sequences</p></li>
                <li><p style="margin-bottom: 0in">non-redundant protein sequences</p></li>
        </ul>
        </li>
</ol>
<ol>
        <li><p style="margin-bottom: 0in"></p></li>
</ol>
<p style="margin-bottom: 0in">Following the establishment of the
pipeline steps, a discussion began on data flow between the stages. 
Early on, it was agreed that an implementation using a central server
as a pipeline coordinator would be simpler and more robust.  The bulk
of the discussion was devoted to whether this central server would
call on each remote pipeline stage to perform the analysis as soon as
a sequence available (a &ldquo;push&rdquo; model), or whether the
central server would make the data available and wait for each
analysis to retrieve its input and upload its output  (a &ldquo;pull&rdquo;
model).  The &ldquo;push&rdquo; model has the advantage of allowing
more rigorous flow control, since the central server has more
knowledge of the running status of each analysis, but requires more
from the remote servers, such as availability for external
connections and the capability to run the analyses in a highly
automated way.  The &ldquo;pull&rdquo; model does not require
external availability or complete automation from the remote pipeline
stages, since they only have to download their input from and upload
their output to the central pipeline server.  Flow control in the
pull model would be by means of pipeline status information made
available by the central pipeline server, tracking what analysis
results are available, and for each analysis, whether its required
inputs are ready for download.</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">Since the &ldquo;pull&rdquo; model
places less of a burden on each remote pipeline stage, it was decided
that (like the medicago annotation project), the tomato distributed
annotation pipeline would be pull-driven.  To simplify
administration, it was also decided that the pipeline should be run
on batches of BACs, rather than individual BACs.</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">Next, a discussion began on the
structure and location of the central annotation result repository. 
It was decided that SGN would house the central repository, and
transfer to and from the repository would be accomplished either with
scp or sftp running over an encrypted ssh2 channel.  An encrypted
transfer scheme was preferred over non-encrypted FTP because it
offers more secure and flexible authentication mechanisms, greater
assurance of data integrity, and acceptable transfer bandwidth
requirements.  The repository will be configured such that all ITAG
participants have accounts and can upload, download, and if necessary
delete files from their assigned parts of the repository.</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">Next, the discussion turned to file
naming conventions. The general conclusion was that BACs in the
annotation pipeline  should be referenced by their <b><span style="font-style: normal">unversioned
</span></b>Genbank accession, which is more unambiguous than their
well plate, row, and column designations, since wells can be
contaminated with other BAC sequences.  The unversioned Genbank
accession is used to allow for keeping the locus names more stable
when the BAC sequence changes.  File names and loci names should also
be based on these Genbank accessions.  Genbank accession-based naming
also has the advantage that the accession tends to be shorter than
the clone name.  Annotation pipeline gene identifiers should thus
start with the Genbank accession, followed by an underline and a
numeric index  number, unique on that BAC.  For alternative splicing,
the splice variants are denoted with a parenthesized letter following
the numeric index number.  This can be followed by a dot and a
version number to denote slightly differently annotated versions of
the same locus.  Version numbers are increased if the underlying BAC
sequence changes.  For example, for the third locus to be annotated
on a fictional BAC AC12310, the second of two alternative
transcripts, and the first version, its identifier might be
&ldquo;AC12310_3(b).1&rdquo;.   This scheme is similar to the one
used in <i>Medicago</i> annotation.</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">The numeric index does not specify a
position on the BAC, but reflects the order in which the gene models
were created. When a new locus is annotated, a new numeric index is
chosen for it that is one greater than the previous highest index
number.  If a gene model is created by merging two older gene models,
the two old gene model identifiers are retired from use and a new
identifier is generated for the merged gene model.  For example, if
AC12310_7.1 is merged with AC12310_11.1, the resulting locus might be
named AC12310_42.1.</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">Thus, adjacent gene models on the
genome will not necessarily have numerically adjacent identifiers,
depending on the order in which loci have been added, removed,
merged, and so forth since the initial assignment of locus names.</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">A predictable file naming scheme is
critical for a pull-based pipeline mechanism.  The following file
naming convention for pipeline result files was formulated and agreed
upon:</p>
<p style="margin-bottom: 0in"><br /></p>
<p align="center" style="margin-bottom: 0in">&lt;versioned
acc.&gt;.&lt;analysis&gt;.itag&lt;pipeline ver.&gt;.v&lt;file
ver.&gt;.&lt;file type&gt;</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">For example,
&ldquo;AC12310.1.repeatmasker_TIGRRepbase.itag12.v3.gff&rdquo; would
be the third version of the file containing the results of running
the analysis 'repeatmasker_TIGRRepbase' on the BAC sequence
AC12310.1, as part of version 12 of the ITAG pipeline.</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">The analysis tags (e.g.
'repeatmasker_TIGRRepbase' or 'eugene') will be determined and
assigned by ITAG in the coming weeks.</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">The ITAG pipeline version is a
particularly important part of the file name.  Since many analyses in
the pipeline depend on the output of other analyses, any change in
the methods used at any step (such as updating reference databases or
changing output formats) will usually require re-running of some or
all of the analyses in the pipeline to ensure that all analysis
results remain directly comparable and consistent with each other. 
Therefore, it will be essential to make these changes in a controlled
and coordinated manner.  It was agreed that each static snapshot of
the analyses and reference datasets used in the pipeline will be
given a pipeline version number, starting from 0 and incrementing by
1 each time <i>any</i> change is
made to the pipeline that may affect any analysis's output.  Pipeline
versions may not be incremented while an analysis batch is in
progress.  Pipeline version increments must be agreed upon
beforehand, and will not be allowed while an annotation batch is in
progress.  It was also agreed that pipeline version 0 should be a
special development version.  While the pipeline is at version 0,
developers are free to change and/or update their pipeline stages
without a pipeline increment.  When the pipeline is considered to be
working and producing good results, the pipeline version will be
incremented to 1 and rigorous pipeline version control will begin.</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">How often should the pipeline be run? 
It was felt that running the pipeline on single BACs would be a waste
of time and a minimum batch size of 10 should be set.  In addition,
to avoid putting too much of a computational burden on our sites, we
also agreed on an initial maximum batch size of 100 BACs.  However,
these limits should be revisited once the pipeline is running and its
performance characteristics are better established.</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">Final gene annotations will be
published primarily in the form of several fasta-format files
containing:</p>
<ul>
        <li><p style="margin-bottom: 0in">protein sequences</p></li>
        <li><p style="margin-bottom: 0in">cds/cdna sequences</p></li>
        <li><p style="margin-bottom: 0in">non-redundant proteins</p></li>
</ul>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">Fasta files will use the following
format for the description lines:</p>
<p style="margin-bottom: 0in"> &gt;&lt;locus name&gt; &lt;functional
description&gt; &lt;versioned seq. acc.&gt;  &lt;evidence codes&gt;
&lt;location on seq&gt; &lt;timestamp&gt;</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in"><b>Locus name:</b><span style="font-weight: medium">
 properly formatted locus name as set out above</span></p>
<p style="margin-bottom: 0in"><b>Functional description:</b><span style="font-weight: medium">
a draft functional description of the locus (obtained from functional
analysis stages of the pipeline)</span></p>
<p style="margin-bottom: 0in"><b>Versioned sequence accession: </b><span style="font-weight: medium">
the versioned Genbank accession of the BAC sequence (e.g. AC12312.1)</span></p>
<p style="margin-bottom: 0in"><b>Evidence codes:</b><span style="font-weight: medium">
string encoding the evidence supporting this annotated locus,
composed of one or more of the following letters:</span></p>
<p style="margin-bottom: 0in">  F - Full length cDNA aligned</p>
<p style="margin-bottom: 0in">  E - EST coverage</p>
<p style="margin-bottom: 0in">  H - homology to an annotation in
another sequenced species</p>
<p style="margin-bottom: 0in">  I - ab initio prediction</p>
<p style="margin-bottom: 0in"><b>Location on sequence:</b><span style="font-weight: medium">
1-based nucleotide coordinate range on the BAC sequence, formatted as
&lt;start&gt;-&lt;finish&gt;.  e.g. 41223-48128</span></p>
<p style="margin-bottom: 0in; font-weight: medium"><br /></p>
<p style="margin-bottom: 0in; font-weight: medium">Therefore, an
example of a properly-formatted description line would be:</p>
<p style="margin-bottom: 0in; font-weight: medium">&gt;AC21353_4(a).2
 putative x-ray vision protein AC21353.1 FEHI 12931-18446
2006-10-31/14:36:22</p>
<p style="margin-bottom: 0in; font-weight: medium"><br /></p>
<p style="margin-bottom: 0in; font-weight: medium"><br /></p>
<p style="margin-bottom: 0in">The annotation of pseudo genes will be
worked out at a later date.</p>
<p style="margin-bottom: 0in">The format for the pseudomolecules to
be used will be worked out at a later date.</p>
<p style="margin-bottom: 0in"><br /></p>
<h3 class="western">Day 3 &ndash; October 25, 2006</h3>
<p style="margin-bottom: 0in">This was a half-day meeting, and was
mostly devoted to clarifications and additions to the decisions made
in the preceding two days.  Minimum and maximum BAC batch sizes were
discussed again briefly, agreeing on an initial minimum and maximum
batch size of 10 and 100 BACs respectively.</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">Additionally, a request by Lincoln
Stein for permission to do a genome-wide annotation using the
ensemble annotation pipeline was discussed.  The decision was made
not to grant permission for him to publish an annotation at this
time, since his analysis pipeline will not be specifically tailored
to tomato, leading to a lower-quality annotation, and it would lead
to confusion about which genome annotation is the &ldquo;official&rdquo;
one.</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">Also, there was a discussion of the
need for a note to be attached to our BAC sequences in Genbank,
asking that people defer genome-wide analyses until our official
annotation comes out.  A consensus was reached that the text of this
note should be discussed and agreed upon at the upcoming SOL project
meeting in November.</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">Next, some clarifications to the
pipeline versioning scheme were made.  The idea of a free-development
pipeline version 0 was introduced (already covered above).  The
mechanics of pipeline synchronization were briefly discussed, with
Rob clarifying that SGN intended to provide both a human-readable web
page showing pipeline status and a machine-readable pipeline status
web service, as described above.</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in">Next came a discussion of arrangements
for further tomato annotation meetings.  An agreement was
reached to hold a tomato annotation meeting at PAG in San Diego in
January.  Also, an agreement was made to try to have a phone
conference of tomato annotators every two weeks.  St&eacute;phane
introduced the VRVS service (<a href="http://www.vrvs.org/">http://www.vrvs.org</a>),
a non-commercial internet conferencing service, as a possible
mechanism for doing this without the cost of international phone
calls.</p>
<p style="margin-bottom: 0in"><br /></p>
<p style="margin-bottom: 0in"><br /></p>

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