<html><head><style>body{font-family:Helvetica,Arial;font-size:13px}</style></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Fantastic. Thanks, Carson. When I use both est2genome and tRNAscan to identify tRNA, I was hoping that both forms of evidence would be used to create a single gene model, which doesn’t seem to be the case. I get duplicate overlapping gene models (one mRNA from est and one tRNA from tRNAscan). Could MAKER merge these models?</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Cheers,</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Shaun</div><p style="color:#000;">On 2014-March-06 at 12:58:50 , Carson Holt (<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>) wrote:</p> <blockquote type="cite" class="clean_bq"><span><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;"><div></div><div>
<title></title>
<div>Yes. I’ll fix the naming.</div>
<div><br></div>
<div>Thanks,</div>
<div>Carson</div>
<div><br></div>
<div><br></div>
<span id="OLK_SRC_BODY_SECTION"></span>
<div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt">
<span id="OLK_SRC_BODY_SECTION"><span style="font-weight:bold">From:</span> Shaun Jackman <<a href="mailto:sjackman@gmail.com">sjackman@gmail.com</a>><br>
<span style="font-weight:bold">Date:</span> Thursday, March 6, 2014
at 1:56 PM<br>
<span style="font-weight:bold">To:</span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br>
<span style="font-weight:bold">Cc:</span> "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>"
<<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject:</span> Re: [maker-devel]
Mapping gene names<br></span></div>
<div><br></div>
<div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
<div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">
Hi, Carson. I agree that identifying non-coding RNA by homology in
general is a non-trivial problem. In my particular case, I have a
well annotated reference species that is very closely related
(99.2% sequence identity), so lifting over the annotations from
that reference species to my species should be pretty straight
forward. It would be great if MAKER had an option for RNA sequence
homology similar to est2genome that does not imply the sequence is
coding.</div>
<div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">
<br></div>
<div id="bloop_customfont" style="margin: 0px;"><span style="color: rgb(0, 0, 0); font-family: Helvetica, Arial; font-size: 13px;">
The integration of MAKER-P with</span> tRNAscan is very useful. The
identified genes are named e.g.
`trnascan-205522-processed-gene-0.38`. tRNA genes are
conventionally named according to the amino acid and anticodon,
such as `trnW-CCA`. Would it be possible for MAKER to name or
perhaps prefix the names with that convention?</div>
<div id="bloop_customfont" style="margin: 0px;"><br></div>
<div id="bloop_customfont" style="margin: 0px;">Cheers,</div>
<div id="bloop_customfont" style="margin: 0px;">Shaun</div>
<p style="color:#000;"><br></p>
<p style="color:#000;">On 2014-March-04 at 18:33:20 , Carson Holt
(<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>)
wrote:</p>
<blockquote type="cite" class="clean_bq">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;">
<div>
<div><span>Trying to call non-coding RNA from ESTs or even sequence
homology is extremely messy (non-trivial problem in most organisms
with high false positive rate), so MAKER for the most part doesn’t
even try to do that. It focuses only on the coding genes.
You can now use tRNAscan and snoscan in the newest version
for some non-coding RNA support (those features were only added a
couple of months ago). So just like other prediction tools
(snap, augustus etc.), the primary focus has always been the coding
genes. We’ve only started adding non-coding RNA support
recently for iPlant, so it’s still relatively
immature.</span></div>
<div><span><br></span></div>
<div><span>Thanks,</span></div>
<div><span>Carson</span></div>
<div><span><br></span></div>
<div><span><br></span></div>
<span><span id="OLK_SRC_BODY_SECTION"></span></span>
<div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt">
<span id="OLK_SRC_BODY_SECTION"><span style="font-weight:bold">From:</span> Shaun Jackman <<a href="mailto:sjackman@gmail.com">sjackman@gmail.com</a>><br>
<span style="font-weight:bold">Reply-To:</span> Shaun Jackman
<<a href="mailto:sjackman@gmail.com">sjackman@gmail.com</a>><br>
<span style="font-weight:bold">Date:</span> Tuesday, March 4, 2014
at 7:10 PM<br>
<span style="font-weight:bold">To:</span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br>
<span style="font-weight:bold">Cc:</span> "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>"
<<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject:</span> Re: [maker-devel]
Mapping gene names<br></span></div>
<div><br></div>
<div dir="ltr">
<div class="markdown-here-wrapper" id="markdown-here-wrapper-554357" style="">
<p style="margin:1.2em 0px!important">Hi, Carson. I set
<code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);background-color:rgb(248,248,248);border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;display:inline">
single_length=50</code>, and it worked like a charm. Thanks for the
tip.</p>
<p style="margin:1.2em 0px!important">The rRNA genes that are found
with est2genome have the feature type set to <em>mRNA</em> and have
corresponding <i>five_prime_UTR</i>, <i>CDS</i> and
<i>three_prime_UTR</i> features. Ideally the feature type would be
set to <i>rRNA</i> or <i>tRNA</i> as appropriate, and would omit
the UTR and CDS features. Is that a feature that you would be
interested in adding to MAKER? The rRNA gene names all start with
“rrn” and the tRNA gene names with “trn”, as is standard, so
determining the appropriate type should be straight forward.</p>
<p style="margin:1.2em 0px!important">Thanks again for your help
with this. Cheers,<br>
Shaun</p>
</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 27 February 2014 17:13, Carson Holt
<span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="auto">
<div>Set single_exon=1, and the minimum size to a smaller value.
I think it's set to 250 right now. Also est2genome is
looking for ORF, so if there is none (as with tRNAs) they probably
won't get picked up.</div>
<div class="">
<div><br></div>
<div>--Carson <br>
<br>
Sent from my iPhone</div>
</div>
<div>
<div class="h5">
<div><br>
On Feb 27, 2014, at 5:27 PM, Shaun Jackman <<a href="mailto:sjackman@gmail.com" target="_blank">sjackman@gmail.com</a>> wrote:<br>
<br></div>
<blockquote type="cite">
<div>
<div dir="ltr">
<div>
<p style="margin:1.2em 0px!important">Sorry, ignore my previous
question. est_forward also carries forward the names of protein
evidence and works like a charm. Thank you!</p>
<p style="margin:1.2em 0px!important">The larger rrn16 and rrn23
genes annotated perfectly, but the smaller rrn4.5 and rrn5 and tRNA
genes didn’t make it into the all.gff file. They are in the blastn
output, and in the evidence_0.gff. rrn5 has perfect identity,
sufficient bits (242 > bit_blastn=40) and sufficient E Value
(2e-66 < eval_blastn=1e-10). How should I debug which filter is
removing these hits?</p>
<pre style="font-family:Consolas,Inconsolata,Courier,monospace;font-size:1em;line-height:1.2em;margin:1.2em 0px">
<code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;white-space:pre-wrap;overflow:auto;border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;border:1px solid rgb(204,204,204);padding:0.5em;color:rgb(51,51,51);background-color:rgb(248,248,255);display:block!important">organism_type=prokaryotic
est2genome=1
protein2genome=1
est_forward=1
</code>
</pre>
<p style="margin:1.2em 0px!important">Cheers,<br>
Shaun</p>
</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 27 February 2014 15:17, Shaun Jackman
<span dir="ltr"><<a href="mailto:sjackman@gmail.com" target="_blank">sjackman@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
<div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">
Is there a corresponding protein_forward=1 option to map
forward protein names from protein2genome?</div>
<div><br></div>
Cheers,
<div>Shaun</div>
<div>
<div>
<div><br>
<p style="color:#a0a0a8">On 2014-February-26 at 15:45:39 , Carson
Holt (<a href="mailto://carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>) wrote:</p>
<blockquote type="cite">
<div dir="auto">
<div>
<div><span>Sorry I meant to say prefilter on the score in the mRNA
column before passing the gff3 to model_gff.</span></div>
<div><span><br></span></div>
<div><span>--Carson <br>
<br>
Sent from my iPhone</span></div>
<div><span><br>
On Feb 26, 2014, at 3:50 PM, Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>> wrote:<br>
<br></span></div>
<blockquote type="cite">
<div>
<div><span>What you can do is run it once with just est_forward=1
and est2genome/protein2genome set to 1. Then take those
results, pass them in as model_gff and use the map_forward option
to then filter the results based on mRNA score and that would copy
names onto new gene under the standard MAKER pipeline.
Eventually it’s really supposed to go into a separate tool
that will map genes onto new assemblies (but under the hood the
tool will just be calling MAKER with certain parameters
restricted). I do this because if people commonly use it
mixed with things like SNAP I can start to get some very weird
behaviors. </span></div>
<div><span><br></span></div>
<div><span>Thanks,</span></div>
<div><span>Carson</span></div>
<div><span><br></span></div>
<div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<span><span style="font-weight:bold">From:</span> Mikael Brandström
Durling <<a href="mailto:mikael.durling@slu.se" target="_blank">mikael.durling@slu.se</a>><br>
<span style="font-weight:bold">Date:</span> Wednesday, February 26,
2014 at 3:04 PM<br>
<span style="font-weight:bold">To:</span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br>
<span style="font-weight:bold">Cc:</span> "<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject:</span> Re: [maker-devel]
Mapping gene names<br></span></div>
<div><br></div>
<div>
<div style="word-wrap:break-word">It seems that this could be a
very useful option in those cases where you have firm a priori
knowledge of the placement of ESTs. However, while trying it I note
that est_forward implies that the est2genome predictor is turned
on, implicitly. Is this necessary for this to work? I’m after the
behavior you describe below where exonerate is made to try really
hard within a limited region to align an est, but I would not like
maker to produce est2genome predictions.
<div><br></div>
<div>In general, I think this maker_coor and est_forward is a
feature set that is worthy to be promoted into a documented
feature.</div>
<div><br></div>
<div>THanks,</div>
<div>Mikael</div>
<div><br>
<div>
<div>26 feb 2014 kl. 17:09 skrev Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>>:</div>
<br>
<blockquote type="cite">
<div style="word-wrap:break-word;font-size:14px;font-family:Calibri,sans-serif">
<div>It will still work without est_forward. It just works a
little differently. Keep in mind this was a hidden feature I
used to find stubborn or hard to find missing genes after
reassembly of a genome.</div>
<div><br></div>
<div>If est_forward is provided, MAKER will parse the database to
look for the maker_coor tags early in the pipeline. Then it
will create a list of locations to search, and it will search them
even if there are no BLAST results to seed the search (normally
MAKER gets a BLAST result first and then polishes it with
exonerate). So maker_coor=chr1 will cause MAKER to look for a
match using all of chr1 as the input to exonerate even when BLAST
finds nothing (this is a very very slow search, but can help pick
up one or two stubborn genes that don’t remap well). To allow
this, MAKER gives exonerate looser matching parameters (i.e. allows
for single base pair introns perhaps caused by assembly errors).
The logic here is that given the fact that I already told
MAKER that with some degree of confidence I expect sequence A to
map to to location X, it will try its hardest to make it
match. </div>
<div><br></div>
<div>Without est_forward set, the maker_coor= flag still gets read
in GI.pm at line 1563, but only after a BLAST alignment has already
seeded it to the region (that BLAST result has the information in
its description parameter). MAKER will then ignore seeds
completely outside of maker_coor. In addition any BLAST seeds that
overlap maker_coor will get the search space for alignment
polishing adjusted to match maker_coor exactly. Also match
parameters for exonerate will not be relaxed as they were with
est_forward.</div>
<div><br></div>
<div>As you can see the behavior, is slightly different (because
it’s an accidental feature).</div>
<div><br></div>
<div>Thanks,</div>
<div>Carson</div>
<div><br></div>
<div><br></div>
<div><br></div>
<div style="font-family:Calibri;font-size:11pt;text-align:left;border-width:1pt medium medium;border-style:solid none none;padding:3pt 0in 0in;border-top-color:rgb(181,196,223)">
<span><span style="font-weight:bold">From:</span> Mikael Brandström
Durling <<a href="mailto:mikael.durling@slu.se" target="_blank">mikael.durling@slu.se</a>><br>
<span style="font-weight:bold">Date:</span> Wednesday, February 26,
2014 at 6:37 AM<br>
<span style="font-weight:bold">To:</span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br>
<span style="font-weight:bold">Cc:</span> "<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject:</span> Re: [maker-devel]
Mapping gene names<br></span></div>
<div><br></div>
<div>
<div style="word-wrap:break-word">That might be a useful and time
saving accidental feature. But, reading the code, it seems that I
need to supply maker_coor but not gene_id, as well as the
configuration option est_forward for this to work. Any occurrences
of maker_coor in GI.pm seems to be conditioned on set_forward=1
right?
<div><br></div>
<div>Mikael</div>
<div><br>
<div>
<div>26 feb 2014 kl. 14:22 skrev Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>>:</div>
<br>
<blockquote type="cite">
<div dir="auto">
<div>Yes. That should work as well as an accidental
feature.</div>
<div><br></div>
<div>--Carson <br>
<br>
Sent from my iPhone</div>
<div><br>
On Feb 26, 2014, at 5:30 AM, Mikael Brandström Durling <<a href="mailto:mikael.durling@slu.se" target="_blank">mikael.durling@slu.se</a>> wrote:<br>
<br></div>
<blockquote type="cite">Can this use of maker_coor be used only to
hint about the placement of the ests, without affecting the naming
of the final genes? Ie if I have a database of EST where I have a
priori knowledge of their rough placement, can this placement be
given to maker without providing est_forward=1?
<div><br></div>
<div>Thanks,</div>
<div>Mikael</div>
<div><br>
<div>
<div>26 feb 2014 kl. 01:58 skrev Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>>:</div>
<br>
<blockquote type="cite">
<div style="word-wrap:break-word;font-size:14px;font-family:Calibri,sans-serif">
<div>There is a way. It’s not a standard option and it’s
undocumented, but if you add est_forward=1 to the
maker_opts.ctl file, then it will do just that. The option
won’t already be there so you’ll have to type it in.</div>
<div><br></div>
<div>There is also a feature designed to work with this option.
If you add tags to your fasta headers, those can be used to
guide the mapping and naming. For example,
gene_id=<some_gene> will ensure different isoforms that
share a common gene_id get clustered into the same gene,
and maker_coor=chr1:1-10000 in the fasta header will force a
particular sequence to only be mapped against chr1 within the range
of 1-10000 bp and just using maker_coor=chr1 will force it to
only be mapped against chr1.</div>
<div><br></div>
<div>This is an undocumented way to remap genes onto new assemblies
using blast alignments of earlier transcript or protein annotations
as a guide.</div>
<div><br></div>
<div>—Carson</div>
<div><br></div>
<div><br></div>
<div><br></div>
<div><br></div>
<div style="font-family:Calibri;font-size:11pt;text-align:left;border-width:1pt medium medium;border-style:solid none none;padding:3pt 0in 0in;border-top-color:rgb(181,196,223)">
<span><span style="font-weight:bold">From:</span> Shaun Jackman
<<a href="mailto:sjackman@gmail.com" target="_blank">sjackman@gmail.com</a>><br>
<span style="font-weight:bold">Reply-To:</span> Shaun Jackman
<<a href="mailto:sjackman@gmail.com" target="_blank">sjackman@gmail.com</a>><br>
<span style="font-weight:bold">Date:</span> Tuesday, February 25,
2014 at 5:06 PM<br>
<span style="font-weight:bold">To:</span> <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject:</span> [maker-devel]
Mapping gene names<br></span></div>
<div><br></div>
<div dir="ltr">
<div>
<p style="margin:1.2em 0px!important">Hi,</p>
<p style="margin:1.2em 0px!important">I’m annotating a genome using
a closely related genome from Genbank, using the .frn (RNA) and
.faa (protein) files from Genbank as evidence to annotate my
genome. I’ve run Maker, and the annotation seems to have worked
well. Is it possible to map the names of the genes from the related
species to my annotation? I see the <em>map_forward</em> option,
which applies to the <em>model_gff</em> parameter. Is there a
similar option for <em>est</em> and <em>protein</em>?</p>
<p style="margin:1.2em 0px!important"><em>maker_opts.ctl</em></p>
<pre style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;font-size:1em;line-height:1.2em;margin:1.2em 0px">
<code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);background-color:rgb(248,248,248);border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;display:inline;white-space:pre-wrap;overflow:auto;border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;border:1px solid rgb(204,204,204);padding:0.5em 0.7em;display:block!important;display:block;padding:0.5em;color:rgb(51,51,51);background-color:rgb(248,248,255);background-repeat:initial initial">est=NC_123456.frn
protein=NC_123456.faa
est2genome=1
protein2genome=1
</code>
</pre>
<p style="margin:1.2em 0px!important">Thanks,<br>
Shaun</p>
</div>
</div>
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