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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/19555?offset=1020</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41736/synvisio-an-interactive-multiscale-synteny-visualization-tool-for-mcscanx</guid>
	<pubDate>Sun, 31 May 2020 02:01:14 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41736/synvisio-an-interactive-multiscale-synteny-visualization-tool-for-mcscanx</link>
	<title><![CDATA[SynVisio: An Interactive Multiscale Synteny Visualization Tool for McScanX.]]></title>
	<description><![CDATA[<p>SynVisio lets you explore the results of&nbsp;<a href="http://chibba.pgml.uga.edu/mcscan2/">McScanX</a>&nbsp;a popular synteny and collinearity detection toolkit and generate publication ready images.</p>
<p>SynVisio requires two files to run:</p>
<ul>
<li>The&nbsp;<strong>simplified gff file</strong>&nbsp;that was used as an input for a McScanX query.</li>
<li>The&nbsp;<strong>collinearity file</strong>&nbsp;generated as an output by McScanX for the same input query.</li>
<li>Optional&nbsp;<strong>track file</strong>&nbsp;in bedgraph format to annotate the generated charts.</li>
</ul>
<p>SynVisio offers different types of visualizations such as&nbsp;<strong>Linear Parallel plots</strong>,&nbsp;<strong>Hive plots</strong>,&nbsp;<strong>Stacked Parallel Plots&nbsp;</strong>and&nbsp;<strong>Dot plots</strong>. Users can configure the type of plots required and then choose the source and the target chromosomes that need to be mapped. Users also have option to download the generated visualizations in publication ready SVG or PNG formats.</p><p>Address of the bookmark: <a href="https://synvisio.github.io/#/" rel="nofollow">https://synvisio.github.io/#/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/33942/mulan-multiple-sequence-local-alignment-and-conservation-visualization-tool</guid>
	<pubDate>Thu, 20 Jul 2017 08:02:32 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/33942/mulan-multiple-sequence-local-alignment-and-conservation-visualization-tool</link>
	<title><![CDATA[Mulan: MUltiple sequence Local AligNment and conservation visualization tool]]></title>
	<description><![CDATA[<p><span>Mulan performs multiple (2 or more) sequence alignments with an efficient and rapid "full local" alignment strategy that ensures a recapitulation of evolutionary sequence rearrangements (such as inversions and reshuffling) in any of the species. It combines&nbsp;</span><a href="http://www.bx.psu.edu/miller_lab/" target="_new"><em>refine</em>&nbsp;and&nbsp;<em>tba</em></a><span>&nbsp;tools to align either "draft" or "finished" quality sequences. Mulan provides a dynamic graphical interface to align and visualize conservation profiles for evolutionarily distant and closely related species.</span><br><span></span></p>
<p><span>Input formats, automated data upload from the&nbsp;</span><a href="http://genome.ucsc.edu/" target="_new">UCSC Genome Browser</a><span>, gene annotation, annotation of repetitive elements, and progress report were previously described in the&nbsp;</span><a href="https://zpicture.dcode.org/zpInstructions.html" target="_zp">zPicture instructions</a><span>&nbsp;and we refer the users to these materials for more details. This introduction is mainly focused on some novel features unique to the Mulan.</span><span><br></span></p><p>Address of the bookmark: <a href="https://mulan.dcode.org/mulanInstructions.php" rel="nofollow">https://mulan.dcode.org/mulanInstructions.php</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/25770/fellowship-doctoral-research-in-biomedical-genomics-including-statistical-genomics</guid>
  <pubDate>Sun, 20 Dec 2015 06:03:43 -0600</pubDate>
  <link></link>
  <title><![CDATA[Fellowship (Doctoral Research In Biomedical Genomics, Including Statistical Genomics)]]></title>
  <description><![CDATA[
<p>Fellowship (Doctoral Research In Biomedical Genomics, Including Statistical Genomics)<br />Eligibility : MSc(Bio-Chemistry, Bio-Informatics, Bio-Tech, Mathematics / Applied Mathematics, Stati, Zoology)<br />Location : Kolkata<br />Last Date : 31 Dec 2015<br />Hiring Process : Written-test</p>

<p>NO: 340/ESTB/ADMN/NIBMG/2015-16 <br />Doctoral Research In Biomedical Genomics, Including Statistical Genomics conduct National Institute of Biomedical Genomics (NIBMG)<br />Information For Students Interested To Pursue Doctoral Research In Biomedical Genomics, Including Statistical Genomics, At The National Institute Of Biomedical Genomics (Nibmg), Kalyan<br />Eligibility conditions for specific areas of research are :<br />Statistical Genomics : An applicant who wishes to pursue research in Statistical Genomics should hold a Master's degree (First class or equivalent) in a relevant discipline (Statistics, Mathematics, Bioinformatics, or a related discipline)<br />Biomedical Genomics : An applicant who wishes to pursue research in any area of biomedical genomics, other than statistical genomics, should hold a Master's degree (First class or equivalent) in a relevant discipline (Biochemistry, Biotechnology, Molecular Biology, Genetics, Zoology, Physiology, or a related discipline)<br />Fellowship : An applicant should have passed the NET conducted by CSIR/UGC/ICMR/DBT within the past ONE year AND should have been awarded a valid Junior Research Fellowship from CSIR, UGC, ICMR, DBT (Category-I only), DST (INSPIRE), NBHM. Preference will be given to candidates with demonstrable research training in the form of summer training or short-term courses in established research laboratories in preparation for a research career in biomedical sciences<br />How to apply<br />Online application will be accepted until 5 PM of December 31, 2015. A formal interview of the short-listed candidates will be held on January 12, 2016</p>

<p>More at http://www.nibmg.ac.in/?q=Career%20Opportunities</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34920/xmatchview-smith-waterman-alignment-visualization</guid>
	<pubDate>Thu, 28 Dec 2017 09:00:58 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34920/xmatchview-smith-waterman-alignment-visualization</link>
	<title><![CDATA[xmatchview: smith-waterman alignment visualization]]></title>
	<description><![CDATA[<p><span>xmatchview and xmatchview-conifer are imaging tools for comparing the synteny between DNA sequences. It allows users to align 2 DNA sequences in fasta format using cross_match and displays the alignment in a variety of image formats. xmatchview and xmatchview-conifer are written in python and run on linux and windows. They serve as visual tools for analyzing cross_match alignments. Cross_match (Green, P. (1994)&nbsp;</span><a href="http://www.phrap.org/">http://www.phrap.org</a><span>) uses an implementation of the Smith-Waterman algorithm for comparing DNA sequences that is sensitive.</span></p>
<p><span>http://www.bcgsc.ca/platform/bioinfo/software/xmatchview</span></p><p>Address of the bookmark: <a href="https://github.com/warrenlr/xmatchview" rel="nofollow">https://github.com/warrenlr/xmatchview</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37527/nanopack-visualizing-and-processing-long-read-sequencing-data</guid>
	<pubDate>Fri, 10 Aug 2018 18:41:34 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37527/nanopack-visualizing-and-processing-long-read-sequencing-data</link>
	<title><![CDATA[NanoPack: visualizing and processing long-read sequencing data]]></title>
	<description><![CDATA[<p>The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at&nbsp;<a href="https://github.com/wdecoster/nanopack" target="">https://github.com/wdecoster/nanopack</a>, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for Linux and are available as a graphical user interface, a web service at&nbsp;<a href="http://nanoplot.bioinf.be/" target="">http://nanoplot.bioinf.be</a>&nbsp;and command line tools.</p>
<p>&nbsp;https://academic.oup.com/bioinformatics/article/34/15/2666/4934939</p><p>Address of the bookmark: <a href="https://github.com/wdecoster/nanoQC" rel="nofollow">https://github.com/wdecoster/nanoQC</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/26568/research-scientist-at-iit-madras</guid>
  <pubDate>Mon, 07 Mar 2016 04:06:13 -0600</pubDate>
  <link></link>
  <title><![CDATA[Research Scientist at IIT Madras]]></title>
  <description><![CDATA[
<p>Research Scientist/Project Associate/Project Assistant Jobs opportunity in Indian Institute of Technology Madras (IIT Madras)</p>

<p>Research Scientist</p>

<p>Qualification : Ph.D in any branch of life science or bioinformatics or computational biology Experience : Previous experience in Molecular Biology, Cell Biology, Biochemistry and Genome/big data analysis is desirable but not mandatory</p>

<p>No. of Vacancy : 02</p>

<p>Project Associate</p>

<p>Qualification : MSc in any branch of life science Experience Previous experience in Molecular Biology, Cell Biology and Biochemistry is desirable but not mandatory</p>

<p>No. of Vacancy : 02</p>

<p>Project Assistant</p>

<p>Qualification : BSc in any branch of life science or chemical science Experience Previous experience any branch in Life science, Molecular Biology, Cell Biology and Biochemistry is desirable but not mandatory</p>

<p>No. of Vacancy : 03<br />How to apply</p>

<p>Interested candidates can forward their profiles to email id: nctb@iitm.ac.in latest by 18th March, 2016</p>

<p>More at https://www.iitm.ac.in/content/national-cancer-tissue-bio-bank-department-biotechnology-iitm-chennai-vacancy-various-post<br />https://www.iitm.ac.in/sites/default/files/notices/vacancy.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38598/zenbu-a-collaborative-omics-data-integration-and-interactive-visualization-system</guid>
	<pubDate>Fri, 04 Jan 2019 13:35:26 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38598/zenbu-a-collaborative-omics-data-integration-and-interactive-visualization-system</link>
	<title><![CDATA[ZENBU: a collaborative, omics data integration and interactive visualization system]]></title>
	<description><![CDATA[<p><span>ZENBU</span><span>&nbsp;</span><span>is a data integration, data analysis, and visualization system enhanced for RNAseq, ChipSeq, CAGE and other types of next-generation-sequence-tag (NGS) based data. ZENBU allows for novel data exploration through "on-demand" data processing and interactive linked-visualizations and is able to make many-views from the same primary sequence alignment data which users can uploaded from BAM, BED, GFF and tab-text files.&nbsp;<br>Please check our&nbsp;<a href="http://fantom.gsc.riken.jp/zenbu/wiki">documentation wiki</a>&nbsp;for details on how to use the system, or check out some of the views above.</span></p><p>Address of the bookmark: <a href="http://fantom.gsc.riken.jp/zenbu/" rel="nofollow">http://fantom.gsc.riken.jp/zenbu/</a></p>]]></description>
	<dc:creator>BioJoker</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44208/circos-visualization</guid>
	<pubDate>Mon, 06 Mar 2023 06:01:32 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44208/circos-visualization</link>
	<title><![CDATA[Circos visualization !]]></title>
	<description><![CDATA[<p>Circos visualization</p>
<p>https://wlcb.oit.uci.edu/modules/index.html</p><p>Address of the bookmark: <a href="https://wlcb.oit.uci.edu/NG-Circos" rel="nofollow">https://wlcb.oit.uci.edu/NG-Circos</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44508/a-web-based-tool-for-sequence-alignment-statistics-and-innovative-visualization</guid>
	<pubDate>Thu, 04 Apr 2024 01:44:50 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44508/a-web-based-tool-for-sequence-alignment-statistics-and-innovative-visualization</link>
	<title><![CDATA[A web-based tool for sequence alignment statistics and innovative visualization]]></title>
	<description><![CDATA[<p>AlignStatPlot, a new R package and online tool that is well-documented and easy-to usefor MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analy-ses on sequencing data and generates new visualisation methods for MSA results. Whencompared to currently available tools, AlignStatPlot provides a robust ability to handle andvisualise diversity data, while the online version will save time and encourage researchersto focus on explaining their findings. It is a simple tool that can be used in conjunction withpopulation genetics software (PDF) AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data.</p><p>Address of the bookmark: <a href="https://bioinformatics.um6p.ma/AlignStatPlot/" rel="nofollow">https://bioinformatics.um6p.ma/AlignStatPlot/</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/26335/ra-at-central-university-of-rajasthan</guid>
  <pubDate>Tue, 09 Feb 2016 03:53:35 -0600</pubDate>
  <link></link>
  <title><![CDATA[RA at Central University of Rajasthan]]></title>
  <description><![CDATA[
<p>Research Fellow Bioinformatics</p>

<p>Eligibility : MSc(Bio-Chemistry, Bio-Informatics, Bio-Tech)</p>

<p>Location : Ajmer</p>

<p>Last Date : 13 Feb 2016</p>

<p>Hiring Process : Face to Face Interview<br />Central University of Rajasthan</p>

<p>Research Fellow Job vacancies in Central University of Rajasthan</p>

<p>Project Title : “Development of natural product derived febrifugine ananlogues as a novel therapeutics against visceral leishmaniasis”</p>

<p>No. of Post : 01</p>

<p>Qualification : Master of Biochemistry, Biotechnology, Bioinformatics and related biological sciences with minimum 55%, Age limit as per government rule.</p>

<p>Desirable Experience : Candidates with experience in cell culture, Chemoinformatics, and Parasitology will be preferred.    </p>

<p>Fellowship : Rs. 25,000/- p.m. consolidated for NET qualified (14,000/- p.m. consolidated for Non-NET)<br />How to apply</p>

<p>The candidates may apply on a plain paper, along with their curriculum vitae (including name, date of birth, academic qualification starting from 10th class, summary of research experience, email id, phone number and passport size photograph) and email to vkprajapati@curaj.ac.in or post the hard copy to the Dr. Vijay Kumar Prajapati PI, DST-SERB Project (YSS/2015/000716), Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Dist- Ajmer, Rajasthan, 305 817 on or before 13th February 2016.</p>

<p>More at http://www.curaj.ac.in/Default.aspx?PageId=241</p>
]]></description>
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