{"id":500,"date":"2011-04-14T13:22:22","date_gmt":"2011-04-14T12:22:22","guid":{"rendered":"http:\/\/www.monkeyshines.co.uk\/blog\/?p=500"},"modified":"2012-02-14T21:31:53","modified_gmt":"2012-02-14T21:31:53","slug":"masamb-xxi-vienna","status":"publish","type":"post","link":"https:\/\/monkeyshines.co.uk\/blog\/masamb-xxi-vienna\/","title":{"rendered":"MASAMB XXI, in Vienna"},"content":{"rendered":"<p>\nI was pleased to be invited to present some of my work at the <a href='http:\/\/www.cibiv.at\/workshops\/masamb11'>MASAMB conference in Vienna<\/a> recently (11-12<sup>th<\/sup> April 2011). My talk was titled &#8220;Quantifying the effect of evolution and genomic alignment on <em>de novo<\/em> RNA gene prediction&#8221;. I have a similarly themed manuscript in preparation, so won&#8217;t go into detail here. But if you have any questions about the presentation, then please get in touch by<br \/>\n<script type=\"text\/javascript\">\n    document.write(String.fromCharCode(60)+\"a href='\"+\"mail\"+\"to:chief_\"+\"monkey\"+String.fromCharCode(64)+\"monkeyshines.c\"+\"o.uk'>email\"+String.fromCharCode(60)+String.fromCharCode(47)+\"a>\");\n<\/script>. The abstract is included below the nice pics.\n<\/p>\n<p>\nI enjoyed both the conference and the time I spent in Vienna, where I appreciated the architecture and culture, as well as the <a href='http:\/\/www.salmbraeu.com\/index.php?id=2&#038;L=1'>beer<\/a> and the wildlife:<br \/>\n<div id='gallery-1' class='gallery galleryid-500 gallery-columns-3 gallery-size-thumbnail'><figure class='gallery-item'>\n\t\t\t<div class='gallery-icon portrait'>\n\t\t\t\t<a href='https:\/\/monkeyshines.co.uk\/blog\/masamb-xxi-vienna\/dsc01075\/'><img loading=\"lazy\" decoding=\"async\" width=\"150\" height=\"150\" src=\"https:\/\/monkeyshines.co.uk\/blog\/wp-content\/uploads\/2011\/04\/DSC01075-e1302779117530-150x150.jpg\" class=\"attachment-thumbnail size-thumbnail\" alt=\"Musikverein\" aria-describedby=\"gallery-1-507\" \/><\/a>\n\t\t\t<\/div>\n\t\t\t\t<figcaption class='wp-caption-text gallery-caption' id='gallery-1-507'>\n\t\t\t\tI saw Gustav Mahler&#8217;s Sixth Symphony here.\n\t\t\t\t<\/figcaption><\/figure><figure class='gallery-item'>\n\t\t\t<div class='gallery-icon landscape'>\n\t\t\t\t<a href='https:\/\/monkeyshines.co.uk\/blog\/masamb-xxi-vienna\/dsc01095\/'><img loading=\"lazy\" decoding=\"async\" width=\"150\" height=\"150\" src=\"https:\/\/monkeyshines.co.uk\/blog\/wp-content\/uploads\/2011\/04\/DSC01095-150x150.jpg\" class=\"attachment-thumbnail size-thumbnail\" alt=\"Sch\u00f6nbrunn gardens\" aria-describedby=\"gallery-1-502\" \/><\/a>\n\t\t\t<\/div>\n\t\t\t\t<figcaption class='wp-caption-text gallery-caption' id='gallery-1-502'>\n\t\t\t\tA too-arty-for-my-own-good shot of the gloriette at Sch\u00f6nbrunn\n\t\t\t\t<\/figcaption><\/figure><figure class='gallery-item'>\n\t\t\t<div class='gallery-icon landscape'>\n\t\t\t\t<a href='https:\/\/monkeyshines.co.uk\/blog\/masamb-xxi-vienna\/dsc01195\/'><img loading=\"lazy\" decoding=\"async\" width=\"150\" height=\"150\" src=\"https:\/\/monkeyshines.co.uk\/blog\/wp-content\/uploads\/2011\/04\/DSC01195-150x150.jpg\" class=\"attachment-thumbnail size-thumbnail\" alt=\"Sch\u00f6nbrunn palm house\" aria-describedby=\"gallery-1-505\" \/><\/a>\n\t\t\t<\/div>\n\t\t\t\t<figcaption class='wp-caption-text gallery-caption' id='gallery-1-505'>\n\t\t\t\tIn the grounds of Sch\u00f6nbrunn palace\n\t\t\t\t<\/figcaption><\/figure><figure class='gallery-item'>\n\t\t\t<div class='gallery-icon portrait'>\n\t\t\t\t<a href='https:\/\/monkeyshines.co.uk\/blog\/masamb-xxi-vienna\/dsc01061\/'><img loading=\"lazy\" decoding=\"async\" width=\"150\" height=\"150\" src=\"https:\/\/monkeyshines.co.uk\/blog\/wp-content\/uploads\/2011\/04\/DSC01061-e1302780676356-150x150.jpg\" class=\"attachment-thumbnail size-thumbnail\" alt=\"Arty &#039;balloon-in-a-tree&#039; shot\" aria-describedby=\"gallery-1-506\" \/><\/a>\n\t\t\t<\/div>\n\t\t\t\t<figcaption class='wp-caption-text gallery-caption' id='gallery-1-506'>\n\t\t\t\tA balloon in a tree in Karlsplatz\n\t\t\t\t<\/figcaption><\/figure><figure class='gallery-item'>\n\t\t\t<div class='gallery-icon portrait'>\n\t\t\t\t<a href='https:\/\/monkeyshines.co.uk\/blog\/masamb-xxi-vienna\/dsc01145\/'><img loading=\"lazy\" decoding=\"async\" width=\"150\" height=\"150\" src=\"https:\/\/monkeyshines.co.uk\/blog\/wp-content\/uploads\/2011\/04\/DSC01145-150x150.jpg\" class=\"attachment-thumbnail size-thumbnail\" alt=\"Red panda\" aria-describedby=\"gallery-1-504\" \/><\/a>\n\t\t\t<\/div>\n\t\t\t\t<figcaption class='wp-caption-text gallery-caption' id='gallery-1-504'>\n\t\t\t\tThe cutest of many cute things in Sch\u00f6nbrunn zoo\n\t\t\t\t<\/figcaption><\/figure><figure class='gallery-item'>\n\t\t\t<div class='gallery-icon portrait'>\n\t\t\t\t<a href='https:\/\/monkeyshines.co.uk\/blog\/masamb-xxi-vienna\/dsc01116\/'><img loading=\"lazy\" decoding=\"async\" width=\"150\" height=\"150\" src=\"https:\/\/monkeyshines.co.uk\/blog\/wp-content\/uploads\/2011\/04\/DSC01116-150x150.jpg\" class=\"attachment-thumbnail size-thumbnail\" alt=\"Sch\u00f6nbrunn privy garden\" aria-describedby=\"gallery-1-503\" \/><\/a>\n\t\t\t<\/div>\n\t\t\t\t<figcaption class='wp-caption-text gallery-caption' id='gallery-1-503'>\n\t\t\t\tThe observant among you can play spot-the-crow\n\t\t\t\t<\/figcaption><\/figure>\n\t\t<\/div>\n\n<\/p>\n<p>\n<b>Quantifying the effect of evolution and genomic alignment on <em>de novo<\/em> RNA gene prediction<\/b>\n<\/p>\n<p>\nJames Allen and Simon Whelan<br \/>\n<br \/>\nUniversity of Manchester, Faculty of Life Sciences, UK\n<\/p>\n<p>\nNon-coding RNA  is biologically  important and  linked  to a  range of diseases, yet  there are potentially many RNA genes of unknown function that do not belong to characterized RNA families. The <em>de novo<\/em> prediction of RNA genes is difficult because  they are heterogeneous, and  tend  to have  fewer restrictions  than protein-coding genes. These problems  are  compounded  by  the  lack  of  independent  datasets  for  benchmarking  predictions.  We  identify alignments of genes from 9 well-defined RNA families in UCSC genomic data for 32 vertebrate species, totaling 296 gene  regions, and use  randomization  to create appropriate negative-control datasets. We evaluate  three popular prediction  programs  (CMfinder,  EvoFold,  and RNAz),  testing  their  ability  to  detect RNA  genes  and  accurately determine gene boundaries. Our  results show  that RNA genes  in genomic alignments have different evolutionary characteristics  to structurally-aware RNA alignments, affecting gene prediction, and provide practical suggestions for the development and application of prediction programs.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>I was pleased to be invited to present some of my work at the MASAMB conference in Vienna recently (11-12th April 2011). My talk was titled &#8220;Quantifying the effect of evolution and genomic alignment on de novo RNA gene prediction&#8221;. I have a similarly themed manuscript in preparation, so won&#8217;t go into detail here. But [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[23,25],"tags":[],"class_list":["post-500","post","type-post","status-publish","format-standard","hentry","category-conferences","category-travel"],"_links":{"self":[{"href":"https:\/\/monkeyshines.co.uk\/blog\/wp-json\/wp\/v2\/posts\/500","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/monkeyshines.co.uk\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/monkeyshines.co.uk\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/monkeyshines.co.uk\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/monkeyshines.co.uk\/blog\/wp-json\/wp\/v2\/comments?post=500"}],"version-history":[{"count":31,"href":"https:\/\/monkeyshines.co.uk\/blog\/wp-json\/wp\/v2\/posts\/500\/revisions"}],"predecessor-version":[{"id":1598,"href":"https:\/\/monkeyshines.co.uk\/blog\/wp-json\/wp\/v2\/posts\/500\/revisions\/1598"}],"wp:attachment":[{"href":"https:\/\/monkeyshines.co.uk\/blog\/wp-json\/wp\/v2\/media?parent=500"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/monkeyshines.co.uk\/blog\/wp-json\/wp\/v2\/categories?post=500"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/monkeyshines.co.uk\/blog\/wp-json\/wp\/v2\/tags?post=500"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}