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<!DOCTYPE html>
<!--[if IE 8]> <html class="no-js lt-ie9" lang="en" > <![endif]-->
<!--[if gt IE 8]><!-->
<html class="no-js" lang="en">
<!--<![endif]-->
<head>
<meta name="generator"
content="HTML Tidy for HTML5 (experimental) for Windows https://github.com/w3c/tidy-html5/tree/c63cc39" />
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width" />
<title>Glimmer WebUI: Search</title>
<link rel="stylesheet" href="css/normalize.css" />
<link rel="stylesheet" href="css/foundation.css" />
<script src="js/vendor/custom.modernizr.js"></script>
<script>
function formSubmit()
{
document.getElementById("glimmer").submit();
}
</script>
</head>
<body>
<nav class="top-bar">
<ul class="title-area">
<!-- Title Area -->
<li class="name">
<h1>
<a href="home.html">Glimmer WebUI</a>
</h1>
</li>
<!-- Remove the class "menu-icon" to get rid of menu icon. Take out "Menu" to just have icon alone -->
<li class="toggle-topbar menu-icon">
<a href="#">
<span>Menu</span>
</a>
</li>
</ul>
<section class="top-bar-section">
<!-- Left Nav Section -->
<ul class="left">
<li class="inactive">
<a href="/bmouler/final/home.html">Home</a>
</li>
<li class="active">
<a href="/bmouler/final/glimmer3.html">Search</a>
</li>
<li class="inactive">
<a href="/bmouler/final/history.html">History</a>
</li>
</ul>
<!-- Right Nav Section -->
<ul class="right">
<li class="inactive">
<a href="http://www.cbcb.umd.edu/software/glimmer/glim302notes.pdf">Release Notes</a>
</li>
<li class="inactive">
<a href="/bmouler/final/references.html">References</a>
</li>
<li class="has-form">
<a class="button" href="http://advanced.jhu.edu/">JHU AAP</a>
</li>
</ul>
</section>
</nav>
<div class="row">
<div class="large-12 columns">
<h2>Glimmer Search</h2>
<p>Leaving optional fields blank will select default values.</p>
<p><a href="#" data-reveal-id="prof_note">Click here for testing instructions.</a></p>
<hr />
</div>
</div>
<form action="/bmouler/final/cgi-bin/run_glimmer.cgi" id="glimmer" method="post" enctype="multipart/form-data">
<div class="row">
<div class="large-12 columns">
<fieldset>
<legend>INPUT</legend>
<div class="large-12 columns">
<p>Upload query sequence in FASTA format:
<input type="file" name="query_seq" /></p><br>
<p>Upload reference sequence in FASTA format <span style="color:gray">[optional]</span>:
<input type="file" name="reference_seq" /></p>
</div>
</fieldset>
</div>
</div>
<div class="row">
<div class="large-12 columns">
<fieldset>
<legend>long-orfs Options</legend>
<div class="large-4 columns">
<div class="row collapse">
<label>Allowable start codons</label>
<div class="small-11 columns">
<input type="text" name="long_orfs_o1" placeholder="Defaults: atg, gtg, ttg" />
</div>
<div class="small-1 columns">
<span data-tooltip class="has-tip postfix" title="Specify allowable start codons as a comma-separated list.">?</span>
</div>
</div>
</div>
<div class="large-4 columns">
<div class="row collapse">
<label>Minimum gene length</label>
<div class="small-11 columns">
<input type="text" name="long_orfs_o2" placeholder="Defaults are automatically calculated..." />
</div>
<div class="small-1 columns">
<span data-tooltip class="has-tip postfix" title="Set the minimum gene length to <em>n</em> nucleotides. This does not include the bases in the stop codon.">?</span>
</div>
</div>
</div>
<div class="large-4 columns">
<div class="row collapse">
<label>Maximum overlap length</label>
<div class="small-11 columns">
<input type="text" name="long_orfs_o3" placeholder="Defaults are automatically calculated..." />
</div>
<div class="small-1 columns">
<span data-tooltip class="has-tip postfix" title="Set the maximum overlap length to <em>n</em>. Overlaps of this many or fewer bases between genes are not regarded as overlaps.">?</span>
</div>
</div>
</div>
<div class="large-4 columns">
<div class="row collapse">
<label>Score cutoff</label>
<div class="small-11 columns">
<input type="text" name="long_orfs_o4" placeholder="Defaults: atg, gtg, ttg" />
</div>
<div class="small-1 columns">
<span data-tooltip class="has-tip postfix" title="Only genes with an entropy distance score less than <em>x</em> will be considered. This cutoff is made before any subsequent steps in the algorithm.">?</span>
</div>
</div>
</div>
<div class="large-4 columns">
<div class="row collapse">
<label>Translation table</label>
<div class="small-11 columns">
<input type="text" name="long_orfs_o5" placeholder="Defaults are automatically calculated..." />
</div>
<div class="small-1 columns">
<span data-tooltip class="has-tip postfix" title="Use Genbank translation table number <em>n</em> to specify stop codons.">?</span>
</div>
</div>
</div>
<div class="large-4 columns">
<div class="row collapse">
<label>Allowable stop codons</label>
<div class="small-11 columns">
<input type="text" name="long_orfs_o6" placeholder="Defaults: tag, tga, taa" />
</div>
<div class="small-1 columns">
<span data-tooltip class="has-tip postfix" title="Specify allowable stop codons as a comma-separated list.">?</span>
</div>
</div>
</div>
<div class="small-2 columns">
<label for="switch1" class="right inline"><span data-tooltip class="has-tip" title="Do NOT automatically calculate the minimum gene length that maximizes the number or length of output regions, but instead use either the value specified by the -g
option or else the default, which is 90.">Fixed gene length</span></label>
</div>
<div class="small-2 columns">
<div class="switch" id="switch1">
<input id="x0" name="long_orfs_s1" type="radio" checked="checked" value="0" />
<label for="x0" onclick="">Off</label>
<input id="x1" name="long_orfs_s1" type="radio" value="1" />
<label for="x1" onclick="">On</label><span></span></div>
</div>
<div class="small-2 columns">
<label for="switch2" class="right inline"><span data-tooltip class="has-tip" title="Assume a linear rather than circular genome, i.e., there will be no “wraparound”
genes with part at the beginning of the sequence and the rest at the end of the sequence.">Linear genome</span></label>
</div>
<div class="small-2 columns">
<div class="switch" id="switch2">
<input id="x2" name="long_orfs_s2" type="radio" checked="checked" value="0" />
<label for="x2" onclick="">Off</label>
<input id="x3" name="long_orfs_s2" type="radio" value="1" />
<label for="x3" onclick="">On</label><span></span></div>
</div>
<div class="small-2 columns">
<label for="switch3" class="right inline"><span data-tooltip class="has-tip" title="Find and use as the minimum gene length the value that maximizes the total length
of non-overlapping genes, instead of the default behaviour, which is to maximize the
total number of non-overlapping genes.">Length option</span></label>
</div>
<div class="small-2 columns">
<div class="switch" id="switch3">
<input id="x4" name="long_orfs_s3" type="radio" checked="checked" value="0" />
<label for="x4" onclick="">Off</label>
<input id="x5" name="long_orfs_s3" type="radio" value="1" />
<label for="x5" onclick="">On</label><span></span></div>
</div>
</fieldset>
</div>
</div>
<div class="row">
<div class="large-12 columns">
<fieldset>
<legend>build-icm Options</legend>
<div class="large-4 columns">
<div class="row collapse">
<label>Depth</label>
<div class="small-11 columns">
<input type="text" name="build_icm_o1" placeholder="Default: 7" />
</div>
<div class="small-1 columns">
<span data-tooltip class="has-tip postfix" title="Set the depth of the ICM to <em>n</em>. The depth is the maximum number of positions
in the context window that will be used to determine the probability of the predicted
position.">?</span>
</div>
</div>
</div>
<div class="large-4 columns">
<div class="row collapse">
<label>Period</label>
<div class="small-11 columns">
<input type="text" name="build_icm_o2" placeholder="Default: 3" />
</div>
<div class="small-1 columns">
<span data-tooltip class="has-tip postfix" title="Set the period of the ICM to <em>n</em>. The period is the number of different submodels
for different positions in the text in a cyclic pattern. E.g., if the period is 3, the first
submodel will determine positions 1,4,7...; the second submodel will determine
positions 2,5,8...; and the third submodel will determine positions 3,6,9... For
a non-periodic model, use a value of 1.">?</span>
</div>
</div>
</div>
<div class="large-4 columns">
<div class="row collapse">
<label>Width</label>
<div class="small-11 columns">
<input type="text" name="build_icm_o3" placeholder="Default: 12" />
</div>
<div class="small-1 columns">
<span data-tooltip class="has-tip postfix" title="Set the width of the ICM to <em>n</em>. The width includes the predicted position.">?</span>
</div>
</div>
</div>
<div class="large-4 columns">
<div class="row collapse">
<label>Translation table</label>
<div class="small-11 columns">
<input type="text" name="build_icm_o4" placeholder="Defaults are automatically calculated..." />
</div>
<div class="small-1 columns">
<span data-tooltip class="has-tip postfix" title="Use Genbank translation table number <em>n</em> to specify stop codons.">?</span>
</div>
</div>
</div>
<div class="large-4 columns">
<div class="row collapse">
<label>Allowable stop codons</label>
<div class="small-11 columns">
<input type="text" name="build_icm_o5" placeholder="Defaults: tag, tga, taa" />
</div>
<div class="small-1 columns">
<span data-tooltip class="has-tip postfix" title="Specify stop codons as a comma-separated list.">?</span>
</div>
</div>
</div>
<div class="small-2 columns">
<label for="switch4" class="right inline"><span data-tooltip class="has-tip" title="Do not use any input strings with in-frame stop codons.">No stops</span></label>
</div>
<div class="small-2 columns">
<div class="switch" id="switch4">
<input id="x6" name="build_icm_s1" type="radio" checked="checked" value="0" />
<label for="x6" onclick="">Off</label>
<input id="x7" name="build_icm_s1" type="radio" value="1" />
<label for="x7" onclick="">On</label><span></span></div>
</div>
<div class="small-2 columns">
<label for="switch5" class="right inline"><span data-tooltip class="has-tip" title="Use the reverse of the input strings to build the ICM. Note that this is merely the reverse and NOT the reverse-complement. In other words, the model is built in the backwards direction.">Reverse</span></label>
</div>
<div class="small-2 columns">
<div class="switch" id="switch5">
<input id="x8" name="build_icm_s2" type="radio" value="0" />
<label for="x8" onclick="">Off</label>
<input id="x9" name="build_icm_s2" type="radio" checked="checked" value="1" />
<label for="x9" onclick="">On</label><span></span></div>
</div>
</fieldset>
</div>
</div>
<div class="row">
<div class="large-12 columns">
<fieldset>
<legend>glimmer3 Options</legend>
<div class="large-4 columns">
<div class="row collapse">
<label>Allowable start codons</label>
<div class="small-11 columns">
<input type="text" name="glimmer3_o1" placeholder="Defaults: atg, gtg, ttg" />
</div>
<div class="small-1 columns">
<span data-tooltip class="has-tip postfix" title="Specify allowable start codons as a comma-separated list.">?</span>
</div>
</div>
</div>
<div class="large-4 columns">
<div class="row collapse">
<label>GC percentage</label>
<div class="small-11 columns">
<input type="text" name="glimmer3_o2" placeholder="Defaults are automatically calculated..." />
</div>
<div class="small-1 columns">
<span data-tooltip class="has-tip postfix" title="Use <em>p</em> as the GC percentage of the independent model, i.e., the model of intergenic sequence. Note: <em>p</em> should be a percentage, e.g., 45.2">?</span>
</div>
</div>
</div>
<div class="large-4 columns">
<div class="row collapse">
<label>Minimum gene length</label>
<div class="small-11 columns">
<input type="text" name="glimmer3_o3" placeholder="Defaults are automatically calculated..." />
</div>
<div class="small-1 columns">
<span data-tooltip class="has-tip postfix" title="Set the minimum gene length to <em>n</em> nucleotides. This does not include the bases in the stop codon.">?</span>
</div>
</div>
</div>
<div class="large-4 columns">
<div class="row collapse">
<label>Maximum overlap length</label>
<div class="small-11 columns">
<input type="text" name="glimmer3_o4" placeholder="Defaults are automatically calculated..." />
</div>
<div class="small-1 columns">
<span data-tooltip class="has-tip postfix" title="Set the maximum overlap length to <em>n</em>. Overlaps of this many or fewer bases are allowed between genes. The new dynamic programming algorithm should never output genes that overlap by more than this many bases.">?</span>
</div>
</div>
</div>
<div class="large-4 columns">
<div class="row collapse">
<label>Probabilities of start codons</label>
<div class="small-11 columns">
<input type="text" name="glimmer3_o5" placeholder="Defaults are automatically calculated..." />
</div>
<div class="small-1 columns">
<span data-tooltip class="has-tip postfix" title="Specify the probability of different start codons (same number and order as in -A
option). If no -A option is given, then there should be 3 values: for atg, gtg and ttg,
in that order. Sample format: -P 0.6,0.35,0.05. If -A is specified without -P, then
each start codon is equally likely (which is very unusual).">?</span>
</div>
</div>
</div>
<div class="large-4 columns">
<div class="row collapse">
<label>Ignore score length</label>
<div class="small-11 columns">
<input type="text" name="glimmer3_o6" placeholder="Defaults are automatically calculated..." />
</div>
<div class="small-1 columns">
<span data-tooltip class="has-tip postfix" title="Consider any gene <em>n</em> or more bases long as a potential gene, regardless of its in-frame
score. Without this option, this value is calculated automatically to be the length
such that the expected number of orfs this long or longer in a random sequence of a
million bases is one.">?</span>
</div>
</div>
</div>
<div class="large-4 columns">
<div class="row collapse">
<label>Threshold score</label>
<div class="small-11 columns">
<input type="text" name="glimmer3_o7" placeholder="Defaults are automatically calculated..." />
</div>
<div class="small-1 columns">
<span data-tooltip class="has-tip postfix" title="Set the threshold score for consideration as a gene to <em>n</em>. If the in-frame score ≥ <em>n</em>,
then the region is given a number and considered a potential gene. Note this is the
integer score in the column labelled “InFrm” in the .detail file, not the decimal
score in the column labelled “Raw”.">?</span>
</div>
</div>
</div>
<div class="large-4 columns">
<div class="row collapse">
<label>Translation table</label>
<div class="small-11 columns">
<input type="text" name="glimmer3_o8" placeholder="Defaults are automatically calculated..." />
</div>
<div class="small-1 columns">
<span data-tooltip class="has-tip postfix" title="Use Genbank translation table number <em>n</em> to specify stop codons.">?</span>
</div>
</div>
</div>
<div class="large-4 columns">
<div class="row collapse">
<label>Allowable stop codons</label>
<div class="small-11 columns">
<input type="text" name="glimmer3_o9" placeholder="Defaults: tag, tga, taa" />
</div>
<div class="small-1 columns">
<span data-tooltip class="has-tip postfix" title="Specify stop codons as a comma-separated list.">?</span>
</div>
</div>
</div>
<div class="small-2 columns">
<label for="switch1" class="right inline"><span data-tooltip class="has-tip" title="Use the first possible codon in an orf as the start codon for initial scoring purposes.
Otherwise, the highest-scoring codon will be used. This only affects the start positions in the .detail file. The final start predictions in the .predict file are always
based on the scoring functions.">First codon</span></label>
</div>
<div class="small-2 columns">
<div class="switch" id="switch6">
<input id="x10" name="glimmer3_s1" type="radio" checked="checked" value="0" />
<label for="x10" onclick="">Off</label>
<input id="x11" name="glimmer3_s1" type="radio" value="1" />
<label for="x11" onclick="">On</label><span></span></div>
</div>
<div class="small-2 columns">
<label for="switch2" class="right inline"><span data-tooltip class="has-tip" title="Assume a linear rather than circular genome, i.e., there will be no genes that
“wraparound” between the beginning and end of the sequence.">Linear genome</span></label>
</div>
<div class="small-2 columns">
<div class="switch" id="switch7">
<input id="x12" name="glimmer3_s2" type="radio" checked="checked" value="0" />
<label for="x12" onclick="">Off</label>
<input id="x13" name="glimmer3_s2" type="radio" value="1" />
<label for="x13" onclick="">On</label><span></span></div>
</div>
<div class="small-2 columns">
<label for="switch3" class="right inline"><span data-tooltip class="has-tip" title="<em>sequence-file</em> is a multifasta file of separate genes to be scored separately, with no
overlap rules. Each sequence is assumed to be in 50
to 30 order and to include the
stop codon.">Separate genes</span></label>
</div>
<div class="small-2 columns">
<div class="switch" id="switch8">
<input id="x14" name="glimmer3_s3" type="radio" checked="checked" value="0" />
<label for="x14" onclick="">Off</label>
<input id="x15" name="glimmer3_s3" type="radio" value="1" />
<label for="x15" onclick="">On</label><span></span></div>
</div>
<div class="small-2 small-offset-4 columns">
<label for="switch3" class="right inline"><span data-tooltip class="has-tip" title="Don’t use the independent probability score column at all. Using this option will
produce more short gene predictions.">No independent probability</span></label>
</div>
<div class="small-2 columns">
<div class="switch" id="switch9">
<input id="x16" name="glimmer3_s4" type="radio" checked="checked" value="0" />
<label for="x16" onclick="">Off</label>
<input id="x17" name="glimmer3_s4" type="radio" value="1" />
<label for="x17" onclick="">On</label><span></span></div>
</div>
<div class="small-2 columns">
<label for="switch3" class="right inline"><span data-tooltip class="has-tip" title="Also score orfs that extend of the end of the sequence(s). This option presumes
that the sequence(s) is linear and not circular. Reported positions of the end of the
sequence are the nearest positions in the correct reading frame. Note that this ignores
any partial codons at the ends of a sequence. Suppose, for example, that a sequence
is 998 bp long and an orf in reading frame +1 starts at position 601 and extends of
the end of the sequence. Then the end of that gene/orf will be reported at position
999, as if the stop codon were in positions 997...999. This is true even if the last two
characters of the sequence are, say, cc and cannot possibly be part of a stop codon.
Any scores associated with orfs that extend past the end of a sequence are computed
using only complete codons contained in the sequence.">Extend</span></label>
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<h4>Here are some FASTA files you can use for testing:</h4>
<p><a href="http://www.ncbi.nlm.nih.gov/nuccore/17154514?report=fasta">Rattus norvegicus strain Brown Norway clone RPCI-31-456P9</a></p>
<p><a href="http://www.ncbi.nlm.nih.gov/nuccore/211588786?report=fasta">Penicillium chrysogenum Wisconsin 54-1255 complete genome, contig Pc00c21</a></p>
<p><a href="http://www.ncbi.nlm.nih.gov/nuccore/479196022?report=fasta">Taylorella equigenitalis 14/56 draft genome</a></p>
<p><a href="http://www.ncbi.nlm.nih.gov/nuccore/17154514?report=fasta">Rattus norvegicus strain Brown Norway clone RPCI-31-456P9</a></p>
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