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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/31881?offset=1290</link>
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	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34141/rami-a-tool-for-identification-and-characterization-of-phylogenetic-clusters-in-microbial-communities</guid>
	<pubDate>Mon, 07 Aug 2017 18:49:27 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34141/rami-a-tool-for-identification-and-characterization-of-phylogenetic-clusters-in-microbial-communities</link>
	<title><![CDATA[RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities]]></title>
	<description><![CDATA[<p>RAMI, which clusters related nodes in a phylogenetic tree based on the patristic distance. RAMI also produces indices of cluster properties and other indices used in population and community studies on-the-fly.</p>
<p><strong>Availability:</strong>&nbsp;RAMI is licensed under GNU GPL and can be run or downloaded from&nbsp;<a href="http://www.acgt.se/online.html" target="">http://www.acgt.se/online.html</a>.</p><p>Address of the bookmark: <a href="https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btp051" rel="nofollow">https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btp051</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22780/ra-bioinformatics-at-institution-centre-for-human-genetics-bangalore</guid>
  <pubDate>Wed, 17 Jun 2015 19:14:37 -0500</pubDate>
  <link></link>
  <title><![CDATA[RA Bioinformatics at Institution: Centre for Human Genetics,  Bangalore]]></title>
  <description><![CDATA[
<p>Institution: Centre for Human Genetics, <br />Bangalore <br />Discipline: Molecular Genetics of Human Disease Biology </p>

<p>Minimum qualification: MSc in any branch of life sciences</p>

<p>Applications are invited for the position of a Research Assistant in the Centre for Human Genetics, Bangalore. </p>

<p>The project involves identification of mutations in MPS (mucopolysaccharidosis) patients, and study of their predicted effects to understand how the mutations lead to disease. </p>

<p>Techniques used will be genomic DNA isolation, PCR, DNA sequencing and sequence analysis. Computational tools would also be used to analyse and interpret data. </p>

<p>Candidates may be assigned work in the ongoing project or in new ones. </p>

<p>The candidate who is selected and joins would acquire hands-on experience in research and the capability to conduct insightful research. </p>

<p>Candidates applying for the position should have an MSc in any branch of life sciences. Those with research experience in cell and molecular biology, and high NET/ GATE score would be preferred. </p>

<p>The successful applicant is expected to stay for at least one and a half years. </p>

<p>Please apply with CV to Sudha Srinivasan (sudha@ibab.ac.in), stating where you saw this ad.</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34594/synima-synteny-imaging-tool</guid>
	<pubDate>Sun, 10 Dec 2017 17:03:48 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34594/synima-synteny-imaging-tool</link>
	<title><![CDATA[Synima: Synteny Imaging tool]]></title>
	<description><![CDATA[<p><span>Synteny Imaging tool (Synima) written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these programs are included with the Synima package, and a pipeline for their use. Synima has a range of graphical parameters including size, colours, order, and labels, which are specified in a config file generated by the first run of Synima &ndash; and can be subsequently edited. Synima runs quickly on a command line to generate informative and publication quality figures. Synima is open source and freely available from&nbsp;</span><span><a href="https://github.com/rhysf/Synima"><span>https://github.com/rhysf/Synima</span></a></span><span>&nbsp;under the MIT License.</span></p><p>Address of the bookmark: <a href="https://github.com/rhysf/Synima" rel="nofollow">https://github.com/rhysf/Synima</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/35885/multi-car-a-tool-of-contig-scaffolding-using-multiple-references</guid>
	<pubDate>Tue, 06 Mar 2018 16:39:41 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/35885/multi-car-a-tool-of-contig-scaffolding-using-multiple-references</link>
	<title><![CDATA[Multi-CAR: a tool of contig scaffolding using multiple references]]></title>
	<description><![CDATA[<p><span>we design a simple heuristic method to further revise our single reference-based scaffolding tool CAR into a new one called Multi-CAR such that it can utilize multiple complete genomes of related organisms as references to more accurately order and orient the contigs of a draft genome. In practical usage, our Multi-CAR does not require prior knowledge concerning phylogenetic relationships among the draft and reference genomes and libraries of paired-end reads. To validate Multi-CAR, we have tested it on a real dataset composed of several prokaryotic genomes and also compared its accuracy performance with other multiple reference-based scaffolding tools Ragout and MeDuSa.&nbsp;</span></p><p>Address of the bookmark: <a href="http://genome.cs.nthu.edu.tw/Multi-CAR/" rel="nofollow">http://genome.cs.nthu.edu.tw/Multi-CAR/</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/22961/bioscripts</guid>
	<pubDate>Sun, 28 Jun 2015 07:46:14 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/22961/bioscripts</link>
	<title><![CDATA[BioScripts]]></title>
	<description><![CDATA[<p>You are requested to please bookmark collection of bioinformatics tools, scripts, codes that can be pieced together in a very easy and flexible manner to perform both simple and complex bioinformatics tasks.</p>
<p>The next-generation sequencing included whole genome sequencing(WGS), transcriptome sequencing (whole cDNA sequencing, RNA-seq), digital gene expression sequencing (Tag-Seq), ChIP-Seq, and so on. And there are many sequencing platform to generate sequece, as well know Sanger/ABi(the frist generation), Solexa/illumina, SOLiD/ABi, 454/Roche. But thier sequence format is different, also they have different error type. High quality data is very important for further analysis or data mining. There are many pipeline for raw sequence quality analysis and control with few of process for reporting reads quality statistical details, trimming, filtering, and error correction. Please bookmarks them for the benefits of bioinformatics community.</p>
<p>https://code.google.com/p/biowiki/</p>
<p>https://code.google.com/p/ngs-pipeline/source/browse/#svn%2Ftrunk</p>
<p>NGSand Perl scripts https://code.google.com/hosting/search?q=NGS+perl&amp;projectsearch=Search+projects</p>
<p>NGS and Python scripts https://code.google.com/hosting/search?q=NGS+Python&amp;projectsearch=Search+projects</p><p>Address of the bookmark: <a href="https://code.google.com/hosting/search?q=bioinformatics&amp;sa=Search" rel="nofollow">https://code.google.com/hosting/search?q=bioinformatics&amp;sa=Search</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36755/minialign-fast-and-accurate-alignment-tool-for-pacbio-and-nanopore-long-reads</guid>
	<pubDate>Thu, 24 May 2018 08:33:26 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36755/minialign-fast-and-accurate-alignment-tool-for-pacbio-and-nanopore-long-reads</link>
	<title><![CDATA[minialign: fast and accurate alignment tool for PacBio and Nanopore long reads]]></title>
	<description><![CDATA[Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining, and SIMD-parallel Smith-Waterman-Gotoh extension.<p>Address of the bookmark: <a href="https://github.com/ocxtal/minialign" rel="nofollow">https://github.com/ocxtal/minialign</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/22995/bioinformatics-phd-postdoc-job-rejection</guid>
	<pubDate>Thu, 02 Jul 2015 08:52:46 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/22995/bioinformatics-phd-postdoc-job-rejection</link>
	<title><![CDATA[Bioinformatics PhD / PostDoc / Job Rejection]]></title>
	<description><![CDATA[<div><p>While your PhD or PostDoc application, it is more common that you got rejected by many professors. Don't disappoint reply it calmly.</p><p><img src="http://bioinformaticsonline.com/mod/photo/rejected1.png" alt="image" style="border: 0px; border: 0px;"></p><p>In grad school, I shared a house with three Bioinformatics PhD students. One, when he applied to a particular professor, received a letter that said, essentially, "If you are applying because you want to enrich yourself, great. If you are applying because you want a job, you should know that you won't get one." I am trying to tell you this is because if you, with a good background in Bioinformatics, are passing up opportunities, you must be a strong candidate in many areas. Enrich yourself.<br /><br /> So, my suggestion is take a deep breath, forgot about all. Don&rsquo;t take it personally. It's been usual processes while hunting for a good lab and professor. Take is positive, I am not sure why they reject, but don't worry perhaps the lab don't deserve you. Always remember there are billions of reasons not to hire someone for projects, especially in a research sector.<br /><br /> My suggestion, please do not whine about how you were a great research candidate for the post, and you just can't understand why they were so stupid as to have rejected you! This feeling will not win you any points in research, community. Especially, when in todays socially connected era everyone is linked. Remember, a nice E-mail saying, "I really wished to working with you on this project and I hope we cross paths again," is all you need to send to the professor. Send a thank you note to the professor. Thank them for the time they spend to judge you. In the future, If you and the professor (of your dream) are attending a bioinformatics conference, invite him/her to lunch (please remember to pay the bill). In today evolving scientific ere, always remember to build your solid network in order to get a job of interest. Join all possible networking sites like LinkedIn, ResearchGate, Acamedia, FB for the same reason. You as a researcher always build a bridge with student/researcher/colleague/professor who have the research potential to lead in research and hire you. Just because you didn't get this project, doesn't mean there isn't another that will open up in couple of month.<br /><br /> Mostly, jobs that are hard to get are hard to get. Only you can decide if the continued sacrifices are worth the expected payout. If it is, keep on plowing. Build relationships. Attend conferences.</p><p>Image ref @ JaSonYa</p></div>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36905/d-genies-a-tool-for-dotplot-large-genomes-in-an-interactive-efficient-and-simple-way</guid>
	<pubDate>Mon, 11 Jun 2018 09:41:22 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36905/d-genies-a-tool-for-dotplot-large-genomes-in-an-interactive-efficient-and-simple-way</link>
	<title><![CDATA[D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way]]></title>
	<description><![CDATA[D-GENIES – for Dotplot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualisation.

We use minimap version 2 to align the two genomes. Then, the PAF file is parsed and plotted into an interactive plot written with d3.js library.

D-Genies also allows to display dot plots from other aligners by uploading their PAF or MAF alignment file.

http://dgenies.toulouse.inra.fr/<p>Address of the bookmark: <a href="http://dgenies.toulouse.inra.fr/" rel="nofollow">http://dgenies.toulouse.inra.fr/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/23209/bisr-jaipur</guid>
  <pubDate>Tue, 07 Jul 2015 23:12:26 -0500</pubDate>
  <link></link>
  <title><![CDATA[BISR Jaipur]]></title>
  <description><![CDATA[
<p>The Bioinformatics Centre at BISR has created an infrastructure for providing facilities to the users working in the field of Biological Sciences. The users of Rajasthan, Jaipur in particular, are using facilities available at the Bioinformatics Centre extensively. The centre has leased line Internet connection as well latest Bioinformatics software for sequence and structure analysis. The centre provides the following services:</p>

<p>    Bioinformatics supports to researchers<br />    Customized training in Bioinformatics for researchers and faculty members<br />    Support in Installing, implementing and maintaining software on computer.<br />    Create awareness for taking preventive measure against data security<br />    Organize workshops on thrust ares of Bioinformatics<br />    Research Training to students of Biotechnology and Bioinformatics </p>

<p>More at http://bioinfo.bisr.res.in/index.php</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37496/gsearch-a-fast-and-flexible-general-search-tool-for-whole-genome-sequencing</guid>
	<pubDate>Mon, 06 Aug 2018 17:19:15 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37496/gsearch-a-fast-and-flexible-general-search-tool-for-whole-genome-sequencing</link>
	<title><![CDATA[gSearch: a fast and flexible general search tool for whole-genome sequencing]]></title>
	<description><![CDATA[<p><span>gSearch compares sequence variants in the Genome Variation Format (GVF) or Variant Call Format (VCF) with a pre-compiled annotation or with variants in other genomes. Its search algorithms are subsequently optimized and implemented in a multi-threaded manner.&nbsp;</span></p><p>Address of the bookmark: <a href="http://ml.ssu.ac.kr/gSearch/index.html" rel="nofollow">http://ml.ssu.ac.kr/gSearch/index.html</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

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