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news-tools.pug
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extends header
block content
body
.wrapper
<!-- ******HEADER****** -->
header.header
.header-main.container
h1.logo.col-md-4.col-sm-4
a(href='https://sunflowergenome.org')
img#logo(src='/images/logo.png', width='300px', height='75px', alt='Logo')
.info.col-md-8.col-sm-8
ul.menu-top.navbar-right.hidden-xs
li.divider
a(href='https://sunflowergenome.org') Home
li.divider
a(href='/faq') FAQ
li
a(href='/contact') Contact
br
include nav-news
<!-- ******CONTENT****** -->
.content.container
.page-wrapper
header.page-heading.clearfix
h1.heading-title.pull-left News
.breadcrumbs.pull-right
ul.breadcrumbs-list
li.breadcrumbs-label You are here:
li
a(href='https://sunflowergenome.org') Home
i.fa.fa-angle-right
li.current News
<!-- breadcrumbs -->
.page-content
.row.page-row
.news-wrapper.col-md-8.col-sm-7
article.news-item
p.meta.text-muted
| By:
a(href='http://rieseberglab.botany.ubc.ca/postdoctoral-fellows/evan-staton/') SES
| | Posted on: 15 Jul 2017
p.featured-image
img.img-responsive(alt='', src='/images/news/annotation-canvfeats-2.jpg')
p.box
| Shown above is a screen capture from the
|
a(href='https://sunflowergenome.org/jbrowse_current/?data=extdata/bronze') genome browser
| displaying expression levels of genes and transposons in a small window on chromosome 1. The transposon annotations in the genome browser and, available for download on this site, were generated with a tool called Tephra which is discussed on this page.
p
| The primary challenge with the assembly and annotation of plant genomes is dealing with repetitive elements such as transposons. The sunflower genome has been particularly challenging due to nature of transposons. That is, most LTR retrotransposons in sunflower are very young, having accumulated since the origin of the species. While much is know about LTR retrotransposons, less attention has been given to other transposon types, in part due to a lack of published tools and methods.
p
| The command line toolkit I have developed, called
|
a(href='https://github.com/sestaton/tephra') Tephra
| , aims to characterize all transposon types in the genome, as well as the structure and diversity of these elements in order to better infer their evolutionary history.
p
| The usage of this tool follows Unix convention where you have a single command with subcommands that perform different functions (similar to samtools). To give an idea of the different utilities provided there is overview of the commands and their description below.
.table-responsive
table.table.table-bordered
thead
tr
th Subcommand
th Description
tbody
tr
td all
td Run all subcommands and generate annotations for all transposon types
tr
td classifyltrs
td Classify LTR retrotransposons into superfamilies and families
tr
td classifytirs
td Classify TIR transposons into superfamilies
tr
td findhelitrons
td Find Helitons in a genome assembly
tr
td findltrs
td Find LTR retrotransposons in a genome assembly
tr
td findnonltrs
td Find non-LTR retrotransposons in a genome assembly
tr
td findtirs
td Find TIR transposons in a genome assembly
tr
td findtrims
td Find TRIM retrotransposons in a genome assembly
tr
td illrecomb
td Characterize the distribution of illegitimate recombination in a genome
tr
td ltrage
td Calculate the age distribution of LTR retrotransposons
tr
td maskref
td Mask a reference genome with transposons
tr
td reannotate
td Transfer annotations from a reference set of repeats to Tephra annotations
tr
td sololtr
td Find solo-LTRs in a genome assembly
tr
td tirage
td Calculate the age distribution of TIR transposons
p.box
| This tool is open source and is available on
|
a(href='https://github.com/sestaton/tephra') github
| , where you can find information about installation and usage.
aside.page-sidebar.col-md-3.col-md-offset-1.col-sm-4.col-sm-offset-1.col-xs-12
section.widget.has-divider
article.news-item.row
figure.thumb.col-md-2.col-sm-3.col-xs-3
img(src='/images/news/expression-thumb-1.jpg', alt='')
.details.col-md-10.col-sm-9.col-xs-9
h4.title
a(href='/news-annotation') HA412HO gene expression browser released
article.news-item.row
figure.thumb.col-md-2.col-sm-3.col-xs-3
img(src='/images/news/jbrowse-thumb-2.jpg', alt='')
.details.col-md-10.col-sm-9.col-xs-9
h4.title
a(href='/news-annotation') Gene and transposon annotations released
article.news-item.row
figure.thumb.col-md-2.col-sm-3.col-xs-3
img(alt='', src='/images/news/browser-thumb-3.jpg')
.details.col-md-10.col-sm-9.col-xs-9
h4.title
a(href='/news-browser') Genome browser updates
section.widget.has-divider
h3.title Upcoming Events
article.events-item.row.page-row
.date-label-wrapper.col-md-3.col-sm-4.col-xs-4
p.date-label
span.month AUG
|
span.date-number 15
.details.col-md-9.col-sm-8.col-xs-8
h5.title Bioinformatics Workshop
p.meta
span.time
i.fa.fa-clock-o
| TBD
br
span.location
i.fa.fa-map-marker
| UBC Main Campus
include footer