tag:blogger.com,1999:blog-59775975440803875972024-03-19T10:51:31.840+01:00Originally 4myths, thoughts and facts about genes and genomes of vertebrates (especially jawless fishes and cartilaginous fishes)Unknownnoreply@blogger.comBlogger94125tag:blogger.com,1999:blog-5977597544080387597.post-16085615253400058462019-09-22T18:41:00.001+02:002019-09-22T18:41:21.269+02:00Do you know Family Tree Mandala ?<div class="css-901oao r-jwli3a r-1qd0xha r-a023e6 r-16dba41 r-ad9z0x r-bcqeeo r-bnwqim r-qvutc0" dir="auto" id="tweet-text" lang="en">
<span class="css-901oao css-16my406 r-gwet1z r-ad9z0x r-bcqeeo r-qvutc0">Do you know Family Tree Mandala? The latest piece '</span><span class="r-18u37iz">Chondrichthyes</span><span class="css-901oao css-16my406 r-gwet1z r-ad9z0x r-bcqeeo r-qvutc0">' has been completed as a result of inspiring collaboration with Takashi Oda</span><span class="r-18u37iz"><a class="css-4rbku5 css-18t94o4 css-901oao css-16my406 r-1n1174f r-1loqt21 r-1qd0xha r-ad9z0x r-bcqeeo r-qvutc0" data-focusable="true" dir="ltr" href="https://twitter.com/studiocorvo" role="link"> @studiocorvo</a></span><span class="css-901oao css-16my406 r-gwet1z r-ad9z0x r-bcqeeo r-qvutc0"></span><span class="css-901oao css-16my406 r-gwet1z r-ad9z0x r-bcqeeo r-qvutc0"> and more talents. </span></div>
<div class="css-901oao r-jwli3a r-1qd0xha r-a023e6 r-16dba41 r-ad9z0x r-bcqeeo r-bnwqim r-qvutc0" dir="auto" id="tweet-text" lang="en">
<span class="css-901oao css-16my406 r-gwet1z r-ad9z0x r-bcqeeo r-qvutc0"> </span></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhYjeRGfCyxxzlodY91EQfYi-ef6E8TPMv0rEeri6cL4kgDk_hpRVvumwSQnd0LBXbPHkiI0990eRRgpyod46bQQVlUXSQzqgTEtLHNCnurMkJk4sBqCo3rMMevsN7wXZskxlzJFh_35wAl/s1600/20190910_235323.jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1200" data-original-width="1600" height="300" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhYjeRGfCyxxzlodY91EQfYi-ef6E8TPMv0rEeri6cL4kgDk_hpRVvumwSQnd0LBXbPHkiI0990eRRgpyod46bQQVlUXSQzqgTEtLHNCnurMkJk4sBqCo3rMMevsN7wXZskxlzJFh_35wAl/s400/20190910_235323.jpg" width="400" /></a></div>
<div class="css-901oao r-jwli3a r-1qd0xha r-a023e6 r-16dba41 r-ad9z0x r-bcqeeo r-bnwqim r-qvutc0" dir="auto" id="tweet-text" lang="en">
<span class="css-901oao css-16my406 r-gwet1z r-ad9z0x r-bcqeeo r-qvutc0"><span class="css-901oao css-16my406 r-gwet1z r-ad9z0x r-bcqeeo r-qvutc0"></span><br /></span></div>
<div class="css-901oao r-jwli3a r-1qd0xha r-a023e6 r-16dba41 r-ad9z0x r-bcqeeo r-bnwqim r-qvutc0" dir="auto" id="tweet-text" lang="en">
<span class="css-901oao css-16my406 r-gwet1z r-ad9z0x r-bcqeeo r-qvutc0">I contributed my expertise of molecular evolution to this amazing joint project. Want one for yourself?</span></div>
<div class="css-901oao r-jwli3a r-1qd0xha r-a023e6 r-16dba41 r-ad9z0x r-bcqeeo r-bnwqim r-qvutc0" dir="auto" id="tweet-text" lang="en">
<span class="css-901oao css-16my406 r-gwet1z r-ad9z0x r-bcqeeo r-qvutc0"> </span><span class="css-901oao css-16my406 r-gwet1z r-ad9z0x r-bcqeeo r-qvutc0"><br /><div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjlsv5eZyQeH9RwNcN_SYeVNAop09ECsMuDCdImBhCANQxfBDHpDF2DSfS6MjyeWlxL6GeZQ3fB_QamWTOkTAYLRMw7TzT-frXc2iCeVptpwGILdP9zoBZSoNwHUHNZilq3InelcQMgKK-x/s1600/20190907_172908.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1200" data-original-width="1600" height="300" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjlsv5eZyQeH9RwNcN_SYeVNAop09ECsMuDCdImBhCANQxfBDHpDF2DSfS6MjyeWlxL6GeZQ3fB_QamWTOkTAYLRMw7TzT-frXc2iCeVptpwGILdP9zoBZSoNwHUHNZilq3InelcQMgKK-x/s400/20190907_172908.jpg" width="400" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
</span><div style="text-align: left;">
<span class="css-901oao css-16my406 r-gwet1z r-ad9z0x r-bcqeeo r-qvutc0"><span class="css-901oao css-16my406 r-gwet1z r-ad9z0x r-bcqeeo r-qvutc0">I really thank people who supported this project through crowdfunding or providing scientific information that my own expertise could not cover. It has not yet widely on sale, but I hope that interested people can get one from anywhere in the world.</span></span><br /><span class="css-901oao css-16my406 r-gwet1z r-ad9z0x r-bcqeeo r-qvutc0"></span></div>
<span class="css-901oao css-16my406 r-gwet1z r-ad9z0x r-bcqeeo r-qvutc0"><div class="separator" style="clear: both; text-align: center;">
<br /></div>
</span></div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-5977597544080387597.post-42218450097354773712019-05-03T18:17:00.000+02:002019-05-03T18:19:26.684+02:00Welcome to Japan - Callorhinchus miliiI am back here after a quite long interval.<br />
<br />
Here is a movie of <i>Callorihnchus milii</i> (ghost shark or elephant fish) very recently introduced in the <a href="https://www.kaiyukan.com/language/eng/">Osaka Aquarium Kaiyukan</a>. <br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<iframe allowfullscreen='allowfullscreen' webkitallowfullscreen='webkitallowfullscreen' mozallowfullscreen='mozallowfullscreen' width='320' height='266' src='https://www.blogger.com/video.g?token=AD6v5dwLyVhsoSVYaWqFdTNaO7QXXNALm4pEr384BsMHgjp73uoIcFiUJYSkMshu2-BS1DZYI-e0yAYStmPfs3LL8Q' class='b-hbp-video b-uploaded' frameborder='0'></iframe></div>
<br />
This species has also been introduced in another aquarium in Ikebukuro, Tokyo.Unknownnoreply@blogger.comtag:blogger.com,1999:blog-5977597544080387597.post-36988718903521285222018-10-14T01:29:00.001+02:002018-10-20T10:37:30.950+02:00Our shark genome analysis paper is outThe shark genome analysis project, conducted with our own initiative as an additional activity, has been <a href="https://www.nature.com/articles/s41559-018-0673-5">published in <i>Nature Ecology & Evolution</i></a>.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjL1mvYtsnCY09Y_m7RKsoOO2wQMlPIIUItPPOHj4jYiXsU1YnL6hbqobsBRTBK0Prg1Db0dtiruvXTjSOyDg8JErYislmsXQpJeFp3QS5qNwS2mmZsEaoMBvc9xGG3a5Xkjw6IIhoZ-602/s1600/3sharks-lateral-new.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" data-original-height="220" data-original-width="1245" height="70" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjL1mvYtsnCY09Y_m7RKsoOO2wQMlPIIUItPPOHj4jYiXsU1YnL6hbqobsBRTBK0Prg1Db0dtiruvXTjSOyDg8JErYislmsXQpJeFp3QS5qNwS2mmZsEaoMBvc9xGG3a5Xkjw6IIhoZ-602/s400/3sharks-lateral-new.jpg" width="400" /></a></div>
<br />
<br />
<br />
<br />
<br />
<br />
Below I share the related resources with researchers in the communities.<br />
<br />
<a href="https://transcriptome.riken.jp/squalomix/">Squalomix</a>: original data archive providing sequence files and similarity searches.<br />
<br />
<a href="https://natureecoevocommunity.nature.com/users/76329-shigehiro-kuraku/posts/39600-decoding-shark-genomes-with-three-species-selected-for-different-reasons">Post in Nat Ecol Evol Community</a>: a story about the paper<br />
<br />
<a href="https://figshare.com/projects/sharkgenome1-phyloinfokobe/28863">Files available at FigShare</a>: gene model GFFs, etc.<br />
<br />
<a href="http://www.riken.jp/en/pr/press/2018/20181009_1/">Official press release</a> from RIKEN<br />
<br />
<br />Unknownnoreply@blogger.comtag:blogger.com,1999:blog-5977597544080387597.post-9590677380537018012017-09-23T06:03:00.000+02:002017-09-23T06:03:27.323+02:00Anole BAC clones availableI have just heard that <a href="https://bacpacresources.org/">BACPAC Resources</a> hosts <a href="http://bacpacresources.org/library.php?id=424">anole lizard BAC libraries</a>, and they can distribute the clones of one's interest. If there is no substantial size of requests, they can quit hosting it. <br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://upload.wikimedia.org/wikipedia/commons/f/fe/Anolis_carolinensis_(male%26female)_by_Robert_Michniewicz.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="520" data-original-width="800" height="207" src="https://upload.wikimedia.org/wikipedia/commons/f/fe/Anolis_carolinensis_(male%26female)_by_Robert_Michniewicz.jpg" width="320" /></a></div>
<br />Unknownnoreply@blogger.comtag:blogger.com,1999:blog-5977597544080387597.post-34417974103731014772016-01-14T16:03:00.000+01:002016-01-14T16:03:36.653+01:00Tree-thinking for non-evolutionary biologists<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgHV1-igQsiMp7Q8256vZLOczyETwFgjq20VS2WI6EfuCUk_Pl599zUC0e8h8vIr6l9dSiutC1JJWPJa_V9Z-gJBG78TvoufurnhDZNCvrtAZqRVlYtNh1WyihFW1IGRTYjnXdUFKCgqlQb/s1600/brcbaumsmith.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgHV1-igQsiMp7Q8256vZLOczyETwFgjq20VS2WI6EfuCUk_Pl599zUC0e8h8vIr6l9dSiutC1JJWPJa_V9Z-gJBG78TvoufurnhDZNCvrtAZqRVlYtNh1WyihFW1IGRTYjnXdUFKCgqlQb/s320/brcbaumsmith.jpg" width="248" /></a></div>
Today I found by chance <a href="http://www.roberts-publishers.com/authors/smith-stacey/tree-thinking-an-introduction-to-phylogenetic-biology.html">the book below titled "Tree-thinking"</a> in a bookshelf in my lab. At that time, I was just looking for other books, but I was attracted by it. This is a trifle, but I wonder if it is just a coincidence that the family name of one of the two authors is 'Baum' (that means 'a tree' in German).<br />
<br />
(Here I stop writing about the 'Tree-thinking' book) <br />
<br />
Recently, I published a review paper titled "<a href="http://onlinelibrary.wiley.com/doi/10.1111/dgd.12258/abstract">Incorporating tree-thinking and evolutionary time scale into developmental biology</a>" with current and past members of my lab, as I was invited to write a review by the journal <i>Development Growth & Differentiation</i>, to contribute to a special issue titled "Time in Development", serving as proceedings of <a href="http://www.cdb.riken.jp/sympo2015/">the symposium</a> held in Kobe, Japan, earlier in Spring 2015.<br />
<br />
I know that herein 'time' means something else, like developmental time course, to many other authors contributing to this issue. To me, it was an ideal form and timing to write about my long-term irritation - underappreciation of basic evolutionary concepts and facts in non-evolutionary studies.<br />
<br />
In the review article, I tried to include as many useful ideas and knowledge as possible. It covers an overview of evolutionary distances between model species frequently used in life sciences with a time scale. I also included some examples of changes of gene repertories among vertebrates - such as Bmp16 and Pax10 genes that I usually call "cryptic pan-vertebrate genes". I hope the review paper help foster evolutionary concepts and skills among a wide range of molecular biologists.Unknownnoreply@blogger.comtag:blogger.com,1999:blog-5977597544080387597.post-55058370276284504782015-12-02T16:53:00.001+01:002015-12-02T16:55:54.729+01:00Optimizing de novo RNA-seq: coordinating library insert length with read lengthMy lab recently published an article on RNA-seq library preparation and assessment of <i>de novo</i> transcriptome results. For this technical improvement, we used the <a href="https://en.wikipedia.org/wiki/Ocelot_gecko">Madagascar ground gecko (or ocelot gecko, <i>Paroedura picta</i>)</a> which is bred in our institute for the purpose of developmental biological studies.<br />
<br />
<h1 style="background-color: white; border: none; clear: both; font-family: Verdana, Arial, Helvetica, sans-serif; line-height: 1.4em; margin: 0px; outline: 0px; padding: 2px 0px 0px; vertical-align: baseline;">
<span style="border-image-outset: initial; border-image-repeat: initial; border-image-slice: initial; border-image-source: initial; border-image-width: initial; border: 0px; font-size: 11px; line-height: 16.5px; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><a href="http://www.biomedcentral.com/1471-2164/16/977">Optimizing and benchmarking <i>de novo</i> transcriptome sequencing: from library preparation to assembly evaluation</a></span></h1>
<h1 style="background-color: white; border: none; clear: both; font-family: Verdana, Arial, Helvetica, sans-serif; line-height: 1.4em; margin: 0px; outline: 0px; padding: 2px 0px 0px; vertical-align: baseline;">
<span style="color: #666666;"><em style="border-image-outset: initial; border-image-repeat: initial; border-image-slice: initial; border-image-source: initial; border-image-width: initial; border: 0px; font-size: 11px; line-height: 16.5px; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">BMC Genomics</em><span style="font-size: 11px; line-height: 16.5px;"> 2015, </span><strong style="border-image-outset: initial; border-image-repeat: initial; border-image-slice: initial; border-image-source: initial; border-image-width: initial; border: 0px; font-size: 11px; line-height: 16.5px; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">16</strong><span style="font-size: 11px; line-height: 16.5px;">:977</span><span class="pseudotab" style="border-image-outset: initial; border-image-repeat: initial; border-image-slice: initial; border-image-source: initial; border-image-width: initial; border: 0px; font-size: 11px; line-height: 16.5px; margin: 0px 0px 0px 20px; outline: 0px; padding: 0px 5px; vertical-align: baseline; white-space: nowrap;">doi:10.1186/s12864-015-2007-1</span></span></h1>
<div>
<span style="color: #666666;"><span class="pseudotab" style="border-image-outset: initial; border-image-repeat: initial; border-image-slice: initial; border-image-source: initial; border-image-width: initial; border: 0px; font-size: 11px; line-height: 16.5px; margin: 0px 0px 0px 20px; outline: 0px; padding: 0px 5px; vertical-align: baseline; white-space: nowrap;"><br /></span></span></div>
<div>
We showed the difference between the length distribution of prepared library inserts and that of actually sequenced fragments. We provide some tips to coordinate the length of library inserts with the read length. For example, we prepared a library starting with RNA fragmentation of 2 and 4 minutes' duration (instead of 8 minutes, according to the TruSeq RNA lib prep protocol), to be sequenced with 2x 171 cycles on HiSeq Rapid Mode (also see <a href="http://www.biotechniques.com/BiotechniquesJournal/2015/May/Optimization-and-cost-saving-in-tagmentation-based-mate-pair-library-preparation-and-sequencing/biotechniques-358351.html">this article</a> for the reason why we do '171 cycles').</div>
<div>
<br /></div>
<div>
The paper deals with post-sequencing steps, too. You may find the <i>de novo</i> assembly part insufficiently explored, and we admit that there would be more programs and settings to test. The strength of the paper rather lies in the assessment of assembly results. For your prior information, a long-standing solution for assembly completeness assessment was the program pipeline, <a href="http://korflab.ucdavis.edu/Datasets/cegma/">CEGMA</a>, developed by the <a href="http://korflab.ucdavis.edu/">Korf Lab</a>. It was announced in May 2015 that CEGMA is no longer supported, and its function is taken over by <a href="http://busco.ezlab.org/">BUSCO</a>. In our paper, we derived a reference gene set consisting of 233 genes conserved throughout vertebrates including sea lamprey and elephant shark (or ghost shark), which can be fed into CEGMA and BUSCO. This new gene set, <a href="http://www.biomedcentral.com/1471-2164/16/977/figure/F3">CVG (core vertebrate genes)</a>, enables more accurate completeness assessment, and especially when used with BUSCO, it saves a lot of time. In fact, in the course of our benchmarks, we noticed suboptimal performances of BUSCO, one of which is the exclusion of cyclostomes and cartilaginous fishes from its original reference gene set, 'vBUSCO' that is supposedly targeting vertebrates.</div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-5977597544080387597.post-17624896217618750992015-05-09T16:03:00.002+02:002015-05-20T07:42:23.389+02:00Our mini-paper introducing iMate ProtocolThe modified protocol from my unit is introduced in a mini-paper <a href="http://www.biotechniques.com/BiotechniquesJournal/2015/May/Optimization-and-cost-saving-in-tagmentation-based-mate-pair-library-preparation-and-sequencing/biotechniques-358351.html">published online</a> in the journal <i>Biotechniques</i>.<br />
<br />
<br />
<b>Optimization and cost-saving in tagmentation-based mate-pair library preparation and sequencing</b><br />
<b>Kaori Tatsumi, Osamu Nishimura, Kazu Itomi, Chiharu Tanegashima, and Shigehiro Kuraku<br /><i>BioTechniques </i>58:253-257 (May 2015) doi 10.2144/000114288</b><br />
<br />
<br />
Therein, we also introduce our strategy to get 80nt-long, 127nt-long or 171nt-long reads using only SBS kits for 50 cycles with HiSeq Rapid Run mode (v1).Unknownnoreply@blogger.comtag:blogger.com,1999:blog-5977597544080387597.post-45402745530850424202015-04-30T17:51:00.001+02:002015-06-07T04:26:49.075+02:00mate pair library prep made 'easy' (?)The word 'easy' is probably not appropriate ... . My team has made some effort to achieve substantial cost-savings and modification to the illumina's Nextera Mate Pair Lib Prep kit.<br />
<br />
It is a 'handy' guide with some tips, based still largely on the manufacturer's protocol. Our guide document is <b><a href="http://www.clst.riken.jp/phylo/imate.html">here</a></b>, and the journal <i><a href="http://www.biotechniques.com/">Biotechniques</a></i> will publish our mini-paper on this soon.<br />
<br />
<iframe allowfullscreen="" frameborder="0" height="510" marginheight="0" marginwidth="0" scrolling="no" src="//www.slideshare.net/slideshow/embed_code/key/AmIwgbkljLsZdg" style="border-width: 1px; border: 1px solid #CCC; margin-bottom: 5px; max-width: 100%;" width="477"> </iframe> <br />
<div style="margin-bottom: 5px;">
<strong> <a href="https://www.slideshare.net/xsighex/imate-protocol-guide-version-12" target="_blank" title="iMate Protocol Guide version 1.2">iMate Protocol Guide version 1.2</a> </strong> from <strong><a href="https://www.slideshare.net/xsighex" target="_blank">Shigehiro Kuraku (工樂 樹洋)</a></strong> </div>
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-5977597544080387597.post-18230957772291564722013-12-28T16:11:00.000+01:002013-12-28T16:11:09.954+01:00Japanese lamprey gene set now available at aLeavesAs announced in the <a href="http://aleaves-update.blogspot.jp/2013/12/update-best-wishes-for-2014.html">change log</a>, I have included the predicted gene set of the Japanese lamprey (<i>Lethenteron japonicum</i>) in the database #6 of <a href="http://aleaves.cdb.riken.jp/aleaves/">aLeaves</a>, the homolog collection tool I have been maintaining. Unknownnoreply@blogger.comtag:blogger.com,1999:blog-5977597544080387597.post-15063093081927910062013-09-12T16:24:00.001+02:002013-09-12T16:24:26.605+02:00Sea Lamprey Consortium Gene Set at aLeavesThe other day I updated the web server I am maintaining, <a href="http://aleaves.cdb.riken.jp/aleaves/">aLeaves</a>, to include latest information for protein-coding genes based on public genome databases.<br />
<br />
The <a href="http://aleaves.cdb.riken.jp/aleaves/database.html#cartilag.faa">database #6</a> at aLeaves now includes the Ensembl gene set and the consortium gene set for the sea lamprey (<i>Petromyzon marinus</i>) genome. It also contain the set of predicted proteins for the elephant shark genome, although the genome assembly for this species is highly incomplete.Unknownnoreply@blogger.comtag:blogger.com,1999:blog-5977597544080387597.post-92014419072985617842013-07-06T03:19:00.002+02:002013-07-06T03:19:52.742+02:003rd International Whale Shark ConferenceThe conference web site is <a href="http://iwsc3.info/">here</a>.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="http://iwsc3.info/"><img border="0" height="242" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgLLeTuvrA8CJLreWWfneatdKmahw4a_KsswLc08fUaVv_Z7SmvIFyL1d8hZNnLcglzIuQ3jBXHAgykmnXPOkIlkjD1bi6IOcK7t1okIiOK_umFmzN3La0kp_LKPl8Az_nuy2oBzaEuGmXQ/s400/GuyHarvey_GA_Aquarium_WhaleShark_Logo_600.jpg" width="400" /></a></div>
<br />Unknownnoreply@blogger.comtag:blogger.com,1999:blog-5977597544080387597.post-3542418420951455562013-07-06T03:04:00.001+02:002013-08-10T05:31:59.383+02:00Tools for NGS analysis - fastq file processingAs I have recently been working (although very slowly) in person on output of the HiSeq1500 in our facility, I needed to look for, test and validate some tools to handle fastq files for various purposes. Below I list some of them for those who are starting or will start this sort of work.<br />
<br />
<br />
<b><i>For various kinds of filtering/trimming</i></b><br />
<br />
<a href="https://github.com/lh3/seqtk">seqtk</a> - a fixed version that retains full sequence names (or 'comments') is <a href="https://github.com/vsbuffalo/seqtk/tree/comment">here</a><br />
[see <a href="http://www.biostars.org/p/75691/">a post</a> at BioStar]<br />
<br />
<a href="http://hannonlab.cshl.edu/fastx_toolkit/commandline.html">fastx-tools</a> (of many tools therein, I am using fastx_trimmer and fastq_quality_filter)<br />
<br />
<a href="http://prinseq.sourceforge.net/manual.html">prinseq</a> (of many options, I use 'trim_left/right' and 'derep')<br />
<br />
<a href="http://code.google.com/p/condetri/">condetri</a> - ... I could not get this working in the way I wanted <br />
<br />
<br />
<b><i>For merging overlapping paired-end reads</i></b><br />
<br />
<a href="http://sourceforge.net/projects/coperead/">cope</a> <br />
<br />
See <a href="http://thegenomefactory.blogspot.jp/2012/11/tools-to-merge-overlapping-paired-end.html">this external blog post</a> (from Nov. 2012) for more info<br />
<br />
<br />
<b><i>For removing adaptor sequences etc.</i></b><br />
<br />
<a href="http://bioinformatics.oxfordjournals.org/content/25/21/2839.full">tagdust</a><br />
<br />
<a href="http://code.google.com/p/cutadapt/">cutadapt</a> - Can't this tool accept multiple adapter sequences in a multifasta file?<br />
<br />
<br />
<b><i>For retrieving paired reads after read filtering </i></b><br />
<br />
<a href="http://compbio.brc.iop.kcl.ac.uk/software/cmpfastq_pe.php">cmpfastq_pe</a><br />
<br />
<br />
<b><i>For removing 'duplicates'</i></b><br />
<br />
<a href="http://code.google.com/p/condetri/downloads/detail?name=filterPCRdupl.pl">filterPCRdupl</a> (I will not use this any more because 'prinseq -derep 4' does the exactly the same thing much faster)<br />
<br />
<br />
<b><i>For validating the tools' functions</i></b><br />
<br />
<a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/">fastqc</a> [ also, <a href="http://www.youtube.com/watch?v=bz93ReOv87Y">a tutorial movie</a> available at YouTube ]<br />
<br />
<a href="http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastq_statistics_usage">fastx_quality_stats</a><br />
<br />
<a href="http://prinseq.sourceforge.net/manual.html#QCAMBIGUOUS">prinseq -stats_all </a><br />
<br />
<br />
There should be more useful tools that I did not list here. Please first google with some key words and look into the <a href="http://seqanswers.com/forums/forumdisplay.php?f=18">'Bioinformatics' forum at SEQanswers</a> to get latest info. Its <a href="http://seqanswers.com/wiki/Software">Wiki page</a> there also provides a list of tools.Unknownnoreply@blogger.comtag:blogger.com,1999:blog-5977597544080387597.post-30194801468912269542013-03-01T13:45:00.001+01:002013-03-01T13:53:14.434+01:00International meeting at CDBThe meeting website is <a href="http://cdb.riken.jp/deepseq2013/index.html">here</a> .<br />
<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh-XsXYht2ev8J4-IAxCIlEQrrNEsY803XbktAOoSljK4F8D-VY1uMNeKW2nyyZCAQw7qJU-6Dc_qGl_R5K1F-AZiIIF7HD0VzU29F5NEyH8_tT9F4DVK2YWEfKP1RnSb2LwbaCKrtXJwtt/s1600/24thCDBMeetingPoster-mm.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh-XsXYht2ev8J4-IAxCIlEQrrNEsY803XbktAOoSljK4F8D-VY1uMNeKW2nyyZCAQw7qJU-6Dc_qGl_R5K1F-AZiIIF7HD0VzU29F5NEyH8_tT9F4DVK2YWEfKP1RnSb2LwbaCKrtXJwtt/s640/24thCDBMeetingPoster-mm.jpg" width="451" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
</div>
<div class="separator" style="clear: both; text-align: center;">
</div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<br />Unknownnoreply@blogger.comtag:blogger.com,1999:blog-5977597544080387597.post-5666798693181146162013-01-29T01:16:00.000+01:002013-01-29T13:43:43.240+01:00Complicated! - lamprey genome resource availabilityI have been asked by many of people around me about publicly available resources of the sea lamprey genome. I have just written down some facts and information on <a href="http://originally4.blogspot.jp/p/sea-lamprey-genome.html">an independent new page inside this blog, titled 'Lamprey genome guide'</a>. The situation is somewhat complicated, I see.<br />
<br />
I will try to keep this page updated for the lamprey researchers' convenience.<br />
I believe this third-party guide does not interfere any database function and research activity by other researchers. But, please let me know if there is some problem.Unknownnoreply@blogger.comtag:blogger.com,1999:blog-5977597544080387597.post-38438088429955268472013-01-26T15:17:00.000+01:002013-01-26T15:17:01.565+01:00'aLeaves' launched !My team has launched a new tool '<a href="http://aleaves.cdb.riken.jp/aleaves/index.html">aLeaves</a>' to allow researchers to collect sequences that are homologous to a query (with NCBI Blast). The motivation to launched it is visualized in an image below. I hope it leads to wider uses of molecular phylogenetics and better understanding about how sequences evolve and how gene families have diversified. I would appreciate any feedback from users of this tool. <br />
<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh1kK2bLCUWBO8FZe5q7feYoeh_3XpUxLhrJMXmw6VEJEwHI5MueGcRMcN8bH68aGKEtj589U-oUmT7TUamEG4NzSxjMjrUfGj95hl8n7c93gGtJvfNAqC_AeuiVF0AbSGpFc-zQpm7T4Cw/s1600/Why-aLeaves.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh1kK2bLCUWBO8FZe5q7feYoeh_3XpUxLhrJMXmw6VEJEwHI5MueGcRMcN8bH68aGKEtj589U-oUmT7TUamEG4NzSxjMjrUfGj95hl8n7c93gGtJvfNAqC_AeuiVF0AbSGpFc-zQpm7T4Cw/s640/Why-aLeaves.gif" width="528" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<br />Unknownnoreply@blogger.comtag:blogger.com,1999:blog-5977597544080387597.post-66750778718576517572012-12-08T14:14:00.001+01:002012-12-08T14:14:08.937+01:00 Indo-Pacific Fish Conference (IPFC)<a href="http://www.fish-isj.jp/9ipfc/">9th Indo-Pacific Fish Conference (IPFC)</a> is going to be held in Okinawa in June 2013.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiTwDFKVn8whrv7qP00IV01ilKuoKELwwpv_ozTTacHgT42yslQ8sR1xI4QGieF_v0-qiLdJEY_gGG1vi3A30A2i3fBeGHR6N2JkBfFXsK0tge1SxI7wjeyzZ6XT8vTfgZu6JwKvpJkz6vG/s1600/header_home.png" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="131" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiTwDFKVn8whrv7qP00IV01ilKuoKELwwpv_ozTTacHgT42yslQ8sR1xI4QGieF_v0-qiLdJEY_gGG1vi3A30A2i3fBeGHR6N2JkBfFXsK0tge1SxI7wjeyzZ6XT8vTfgZu6JwKvpJkz6vG/s400/header_home.png" width="400" /></a></div>
<br />Unknownnoreply@blogger.comtag:blogger.com,1999:blog-5977597544080387597.post-79725659252188886642012-10-03T14:50:00.001+02:002012-10-14T15:42:59.515+02:00Bioinformatician position advertised!My unit is looking for an individual skilled with large-scale sequence data handling.<br />
<br />
The detail is found here:<br />
<a href="http://seqanswers.com/forums/showthread.php?t=23818">http://seqanswers.com/forums/showthread.php?t=23818</a><br />
<br />
<a href="http://www.nature.com/naturejobs/science/jobs/286326-A-bioinformatician-postdoc-or-technical-staff-at-sequencing-core-unit-of-RIKEN-Center-for-Developmental-Biology%20">http://www.nature.com/naturejobs/science/jobs/286326-A-bioinformatician-postdoc-or-technical-staff-at-sequencing-core-unit-of-RIKEN-Center-for-Developmental-Biology </a><br />
<br />
Please feel free to contact to the email address therein for questions etc.Unknownnoreply@blogger.comtag:blogger.com,1999:blog-5977597544080387597.post-17649324268651754762012-08-26T15:32:00.000+02:002012-08-26T15:32:46.136+02:00Recent addition to my collectionAfter I moved to Japan in early Spring, I visited aquarium parks in Japan several times. The most impressive one was that in Okinawa, <a href="http://oki-churaumi.jp/en/index.html">Churaumi Aquarium</a>.<br />
<br />
The newest one I visited was that in Tokyo, <a href="http://www.sumida-aquarium.com/en/">Sumida Aquarium</a>. This one was just opened in May 2012, beside the Tokyo Skytree also just opened at the same time.<br />
<br />
The below are the miniature figures I bought in the souvenir shop in the Sumida Aquarium. On the left you see the zebra shark (<i>Stegostoma fasciatum</i>), and on the right, the leopard shark (<i>Triakis semifasciata</i>). <br />
<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj9QAO5HAM4hUx-mOwU4kNgonaHg0xTH28ltHlFtIH2zOuGS8wFNUw2IjjwwZBYUWhD7Yt_bvdFEErv8ciE1XGoENivoulM4hbOqci_DGHrdjHkHTYmM0M8TApxC-3zy6RBhHh2ljdP4mcs/s1600/2012-08-05+09.23.05.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="300" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj9QAO5HAM4hUx-mOwU4kNgonaHg0xTH28ltHlFtIH2zOuGS8wFNUw2IjjwwZBYUWhD7Yt_bvdFEErv8ciE1XGoENivoulM4hbOqci_DGHrdjHkHTYmM0M8TApxC-3zy6RBhHh2ljdP4mcs/s400/2012-08-05+09.23.05.jpg" width="400" /></a></div>
<br />
The one on the right is my favorite. I didn't expect that I can find figures for these species at all. I got very excited and ended up with spending two thousand yen for them.<br />
<br />
<br />Unknownnoreply@blogger.comtag:blogger.com,1999:blog-5977597544080387597.post-69115859871963590492012-08-17T02:07:00.004+02:002012-08-17T02:07:58.540+02:00EEA 2012 in Milan, ItalyEuropean Elasmobranch Association’s 16th Annual Conference will be held in Milan, Italy, 22th-25h November 2012. [ <a href="http://www.sibm.it/NUOVO_GRIS/EEA.html">conference web site</a> ]<br />
<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjRpj9A3_980haab0OMl1AWy3aVfP5GMeJPzULFs2lVgjrE62MO9dG7Fq3PAYSyU5-FoUDS3r2GmkOznsEw4hkJd3hoaQ8tl_aGSBrVvEKT8-Xl-x3q08elSfrsu5sbHzaSoAeYZ-m4Mdez/s1600/EEA_2012_logo_frei2.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="168" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjRpj9A3_980haab0OMl1AWy3aVfP5GMeJPzULFs2lVgjrE62MO9dG7Fq3PAYSyU5-FoUDS3r2GmkOznsEw4hkJd3hoaQ8tl_aGSBrVvEKT8-Xl-x3q08elSfrsu5sbHzaSoAeYZ-m4Mdez/s320/EEA_2012_logo_frei2.gif" width="320" /></a></div>
<br />Unknownnoreply@blogger.comtag:blogger.com,1999:blog-5977597544080387597.post-26970639155829440692012-08-11T13:57:00.001+02:002012-08-11T13:58:09.527+02:00My education restarted - Day 1About 6 months after I quited working in a university in Southern Germany, I gave the first lecture in front of students this week. It was part of the 1-week-long undergrad internship program that the institute hosted. I had students raise their hands for several questions.<br />
<br />
They included a basic question, 'Have you had any bioinformatics lecture in your university study?' <br />
<br />
Out of 23 very keen students (primarily interested in developmental biology, though), .......................... only 3 raised their hands.<br />
<br />
It will take time, but I have to seriously think about how to change this reality.Unknownnoreply@blogger.comtag:blogger.com,1999:blog-5977597544080387597.post-51456556089049687452012-08-04T15:48:00.001+02:002012-08-04T15:48:28.674+02:00History to make ... - from Olympic gamesI am quietly excited about the rise of Japanese soccer - both mens' and womens'. I did not imagine that the day like this really comes. But, what is really new and what has changed? In my sense, nothing really. Especially, in the mens' team, there is not a single special player. They just have unity, patience and skills. These elements are also what I truly respect in my work, especially in what I am now trying to achieve in my new position in Japan.Unknownnoreply@blogger.comtag:blogger.com,1999:blog-5977597544080387597.post-32272821804552929542012-07-18T01:03:00.002+02:002012-07-18T01:03:12.266+02:00Nonsense to compare, but ...I always get puzzled when I am asked 'which do you like, life in Germany or Japan?'. But, I can easily list differences between them.<br />
<br />
On the other hand, there are many things that I previously did not take as advantage of living in Japan. New discoveries!! One of them is that I can access to every kind of research expertise in the country because many, many people live in the small islands (=Japan).<br />
<br />
When I was in southern Germany, I felt that I was in the middle of many pretty cities with various research centers and researchers in Switzerland, France, Austria, and of course Germany. But, in fact they were scattered throughout the vast land. <br />
<br />
Here in Japan, in the small islands, we have access to all kinds of things, and that is convenient. But, this is the reason why the country tends (or I should say 'we tend'?) to become isolated from the rest of the world. I am seeing all the pros and cons of this tendency.<br />
<br />
from <a href="http://en.wikipedia.org/wiki/Yokohama">Yokohama</a>Unknownnoreply@blogger.comtag:blogger.com,1999:blog-5977597544080387597.post-10625164004848322782012-06-15T02:52:00.001+02:002012-06-15T02:57:04.371+02:00Skate genome resourceThe journal DATABASE published <a href="http://database.oxfordjournals.org/content/2012/bar064.full">an article about skate genome annotation</a>. It includes links to the <a href="http://skatebase.org/">project website</a> and <a href="http://0-www.ncbi.nlm.nih.gov.ilsprod.lib.neu.edu/Traces/wgs/?&val=AESE&size=50&page=59248">sequence resources</a> .Unknownnoreply@blogger.comtag:blogger.com,1999:blog-5977597544080387597.post-71252952429047335582012-06-08T16:13:00.000+02:002013-07-25T16:14:45.568+02:006 - 0 for JapanThe <a href="http://www.fifa.com/worldcup/preliminaries/asia/teams/team=43819/index.html">match between Japan and Jordan</a> was played in Saitama, Japan. The number 10 of the Japanese team, Shinji Kagawa, is moving to Manchester United after scoring 13 goals this year for Borussia Dortmund (BVB!) in Germany. He also scored one goal tonight.Unknownnoreply@blogger.comtag:blogger.com,1999:blog-5977597544080387597.post-82039899357100222542012-05-17T15:41:00.001+02:002012-05-17T15:42:33.424+02:00RIKEN CDB Graduate School GuidanceOn May 26th, RIKEN CDB in Kobe, Japan, will hold the first annual guidance session for students who want to start developmental biology research for master or doctor program.<br />
<br />
Because targeted participants are probably already in Japan, I paste below the official advertisement written in Japanese. I will also join this event and introduce my unit.<br />
<br />
----<br />
<br />
<pre wrap="">神戸にある理研 発生・再生総合研究センター(CDB)では、5月26日(土曜午後)に連携大学院説明会を開くことになりました。<a class="moz-txt-link-freetext" href="http://www.cdb.riken.jp/daigakuin/">http://www.cdb.riken.jp/daigakuin/</a>
この説明会は、理研 発生・再生総合研究センター(CDB)中で、大学院の講座として、大学院生も行ける研究室を紹介しようというもので、今年が初めての試みです。遠隔地からも参加してもらえるよう、午後12時50分から開始します。CDBを代表するサイエンティストのレクチャーや連携大学院の教員を兼ねているラボの訪問の機会ももうけてあります(プラス懇親会)。
</pre>
<br />
<div class="separator" style="clear: both; text-align: center;">
<img border="0" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj8Bzo2RUiyPftpwBy4cR6P1uULwHlbn5CQ0-9GEIGK_DmUT6QEV-cbvj99X3_XSrGYyjhtxQ4RUUTdQPe-7QUq0ANZOZoktljiFaO98n1-WEu4wXFet0M_RHxkeUUa-EVUVWPg9BtpFZRH/s640/poster-final.jpg" width="452" /></div>
<br />
大学院を決めようとしている学部学生(4年)と修士の学生に広くこの説明会の存在を知ってもらいたいので、mailing list, twitter、facebookを使っている方、あるいは、みなさんのラボの後輩や、そのまた後輩の学部学生に、この情報を伝えていただければ大変ありがたく思います。<br />
<br />
ぜひよろしくお願いします。Unknownnoreply@blogger.com