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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/28117?offset=870</link>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/9598/junior-research-fellowship-at-gb-pant-university</guid>
  <pubDate>Thu, 03 Apr 2014 12:29:46 -0500</pubDate>
  <link></link>
  <title><![CDATA[Junior Research Fellowship at G.B. PANT UNIVERSITY]]></title>
  <description><![CDATA[
<p>DEPARTMENT OF MOLECULAR BIOLOGY &amp; GENETIC ENGINEERING<br />COLLEGE OF BASIC SCIENCE AND HUMANITIES<br />G.B. PANT UNIVERSITY OF AGRICULTURE AND TECHNOLOGY<br />PANTNAGAR -263145, UTTARAKHAND</p>

<p>No. CBSH/MBGE/356</p>

<p>Subject: Advertisement for the award of Junior Research Fellowship.</p>

<p>Applications are invited for award of one Junior Research Fellowship on a consolidated fellowship of Rs. 12,000/- pm in the project “Bioinformatics Sub-DIC ”, under the Coordinatorship Dr. Anil Kumar. The fellowship is purely temporary and may continue till the duration of the project or maximum three years which ever is earlier. The appointment shall be given on six monthly review basis.</p>

<p>ESSENTIAL QUALIFICATION</p>

<p>M.Sc. Bioinformatics having research experience on In silico experimentation.</p>

<p>Candidates possessing the above qualifications may submit their application on<br />plain paper in the following format to the undersigned latest 18 April, 2014 the interviews will be held on 19 April, 2014 at 11.00 AM in the office of the undersigned. No separate letter for interview will be issued or any TA/DA will be paid for attending the interview.</p>

<p>Advertisement: http://www.gbpuat.ac.in/01042014_18april14_Advertisement%20for%20JRF%20Position,%20BI.pdf</p>
]]></description>
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	<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/9859/bioinformatics-jrfsrf-position-at-university-of-hyderabad</guid>
  <pubDate>Tue, 15 Apr 2014 20:07:52 -0500</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics JRF/SRF position at University of Hyderabad]]></title>
  <description><![CDATA[
<p>UNIVERSITY OF HYDERABAD SCHOOL OF LIFE SCIENCES </p>

<p>Applications are invited from qualified individuals for a JRF/SRF position (sponsored by DBT/DST) at Prof. Jagan Pongubala’s laboratory, University of Hyderabad. Dr. Pongubala’s laboratory is investigating the molecular pathways that control the development of innate and adaptive immune cell types utilizing a combination of genetic, molecular and computational approaches.</p>

<p>JRF/SRF</p>

<p>Masters degree in Bioinformatics  (M.Sc./M.Tech.)</p>

<p>Rs. 12,000+HRA<br />Rs. 16,000+HRA</p>

<p>Initial appointment is for one year and  subjected to renewal up to 2 years</p>

<p>Candidates selected for the above position would have a choice to work on computational biology or experimental  biology. Candidates interested to work on computational biology are expected to perform high-throughput sequencing  (NGS) data analysis and should have a strong background in Bioinformatics &amp; Computational Biology, good  programming skills particularly Perl, Python, R and work experience in Linux environment.</p>

<p>Candidates interested to work on experimental biology should have work experience in techniques that are routinely  used in molecular biology and mammalian cell culture. A basic knowledge of bioinformatics is also desired. </p>

<p>Applicants for the above positions should have a Masters degree (M.Tech/M.Sc) with an aggregate marks greater  than 70% or a 7.5 CGPA. Candidates having JRF-fellowship through CSIR/UGC/ICMR/DBT will be encouraged  to enroll into Ph.D. program. The interested candidates having excellent organizational skills and the ability to work  in a team environment with an aspiration to learn new techniques and explore new scientific areas are requested to generate their resume using the link https://cvmkr.com/CV/new#0 and forward to pongubalajagan@gmail.com</p>

<p>Review of applications will begin immediately and continue until the position is filled. Eligible candidates will be called for an interview. No TA/ DA will be paid for attending the interview or at the time of joining the post. Applicants should note that the appointment is purely temporary and subjected to renewal up to three years and there is no Right to Claim for any regular appointment with the University.</p>

<p>Corresponding address: Jagan Pongubala, Ph.D.<br />Department of Animal Sciences<br />School of Life Sciences, Room:S44<br />University of Hyderabad<br />Gachibowli, Hyderabad 500046</p>

<p>Advertisement: https://www.uohyd.ac.in/images/recruitment/jrf-srf_130414.pdf</p>
]]></description>
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	<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>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/10124/jrf-at-bose-institute-kolkata</guid>
  <pubDate>Mon, 21 Apr 2014 19:41:14 -0500</pubDate>
  <link></link>
  <title><![CDATA[JRF at Bose Institute, Kolkata]]></title>
  <description><![CDATA[
<p>ADVT. No. S/BIC/01/2014-15</p>

<p>Bose Institute, Kolkata, invites applications from Indian Citizens for ONE (01) temporary position of Junior Research Fellow in the DBT sponsored project entitled, “Centre of Excellance (CoE) in Bioinformatics at Bose Institute”, running under Prof. Pinakpani Chakrabarti, Project Co-ordinatior, Bioinformatics Centre. The project is tenable upto 31.03.2017, but duration of the fellowship is one year only. The JRF will work with one of the faculty members of the center based on his / her motivation in any specific area on Bioinformatics.</p>

<p>Essential Qualification: 1st class M.Sc. / M.Tech degree in any stream of Chemical/ Biological Sciences with CSIR-UGC-NET-JRF / ICMR-JRF / DBT-JRF or CSIR-UGCNET- LS / GATE qualification.</p>

<p>Desirable qualification:</p>

<p>(i) Specialized knowledge in Organic / Physical chemistry.<br />(ii) Any exposure to research involving the small molecules (like drug) and / or protein structure determination or prediction.<br />(iii) Basic knowledge in computer programming, e.g. using FORTRAN, C, shell, perl etc.<br />(iv) Hands-on-experience on any of the following software : CHARMM/AMBER/NAMD/GROMACS,Gaussian/Gamess, Haddock/Autodock, Schrodinger etc. (or any other software serving similar purposes in molecular modeling)</p>

<p>Fellowship :</p>

<p>(i) Rs. 16,000/- p.m., plus admissible HRA &amp; Medical Benefit for M.Sc. with CSIRUGC NET-JRF/ICMR-JRF/DBT-JRF or M.Tech. with CSIR-UGC NETJRF/<br />ICMR-JRF/DBT-JRF/CSIR-UGC NET-LS/GATE<br />(ii) Rs. 12,000/- p.m., plus admissible HRA &amp; Medical Benefit for M.Sc. with CSIRUGC NET-LS/GATE</p>

<p>Age : Below 28 years as on the day on which the application is made (relaxable in case of SC/ST/OBC/WOMEN candidates only as per rule).</p>

<p>Interested and eligible candidates should apply on plain paper duly signed by them clearly mentioning the area of interest in research, possession of any desirable qualification (s) as mentioned above and quoting Advertisement No. on the envelop as well as application with complete Bio-data giving e-mail ID, Phone No. and details of qualification i.e. examination passed, year, division, percentage of marks, from Secondary onwards with attested copies of testimonials, addressed to the Registrar, Bose Institute, P-1/12, CIT Scheme VII-M, Kankurgachi, Kolkata-700054 on or before April 25, 2014.</p>

<p>The shortlisted candidates will be called for an interview. Applicants are advised to check our website for future updates.</p>

<p>Advertisement: www.boseinst.ernet.in/ADVT/14/p_2.pdf</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36935/assemblytics-delta-file-to-analyze-alignments-of-an-assembly-to-another-assembly-or-a-reference-genome</guid>
	<pubDate>Thu, 14 Jun 2018 07:31:00 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36935/assemblytics-delta-file-to-analyze-alignments-of-an-assembly-to-another-assembly-or-a-reference-genome</link>
	<title><![CDATA[assemblytics: delta file to analyze alignments of an assembly to another assembly or a reference genome]]></title>
	<description><![CDATA[Download and install MUMmer
Align your assembly to a reference genome using nucmer (from MUMmer package)
$ nucmer -maxmatch -l 100 -c 500 REFERENCE.fa ASSEMBLY.fa -prefix OUT
Consult the MUMmer manual if you encounter problems

Optional: Gzip the delta file to speed up upload (usually 2-4X faster)
$ gzip OUT.delta
Then use the OUT.delta.gz file for upload.
Upload the .delta or delta.gz file (view example) to Assemblytics
Important: Use only contigs rather than scaffolds from the assembly. This will prevent false positives when the number of Ns in the scaffolded sequence does not match perfectly to the distance in the reference.

The unique sequence length required represents an anchor for determining if a sequence is unique enough to safely call variants from, which is an alternative to the mapping quality filter for read alignment.

http://assemblytics.com/<p>Address of the bookmark: <a href="http://assemblytics.com/" rel="nofollow">http://assemblytics.com/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/10262/research-fellow-phd-candidate-in-computational-biology-%E2%80%93-2-positions</guid>
  <pubDate>Fri, 25 Apr 2014 20:19:58 -0500</pubDate>
  <link></link>
  <title><![CDATA[Research fellow (PhD candidate) in computational biology – 2 positions]]></title>
  <description><![CDATA[
<p>At the Department of Informatics two 4-year positions as research fellow are available in the field of computational biology connected to the Computational Biology Unit. The positions are linked to the project “Integrated genomics - linking transcriptional and translational regulation over developmental time” supported by the Bergen Research Foundation</p>

<p>The fate of a cell is ultimately the product of the regulation of its genes. Gene regulation is a coordinated process acting at multiple levels of which transcription and translation are the most prominent. The Valen group is dedicated to the fundamental question of how transcription and translation is integrated to obtain the desired protein abundance. The recent development of high-throughput next generation sequencing techniques to monitor both active translation and transcription has made it possible to study this connection at the genome scale.</p>

<p>This project aims to elucidate the links between regulation of translation and transcription. The applicant will analyze next generation sequencing data and model gene regulation on a genome-wide level to identify the features that affect the translational output of transcripts. The work will be done in close collaboration with experimental scientists who will test the predictions of the computational models.</p>

<p>Additional information on the position can be obtained by contacting Eivind Valen (eivind.valen@ii.uib.no).</p>

<p>The research fellow must take part in the University’s approved PhD program leading to the degree within a time limit of 3 years. Application for admission to the PhD program, including a project plan outline for the training module, will be worked out in collaboration with the research group in question.</p>

<p>In total, the fellowship period is 4 years, 25 % of this will be allocated to teaching and/or administrative duties. The fellowship period may be reduced if the successful applicant has held previous employment as a research fellow or similar.</p>

<p>http://www.jobbnorge.no/en/available-jobs/job/102235/research-fellow-phd-candidate-in-computational-biology-2-positions</p>
]]></description>
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	<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>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/10415/bioinformatician-stuck-in-wet-lab</guid>
	<pubDate>Tue, 06 May 2014 12:46:56 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/10415/bioinformatician-stuck-in-wet-lab</link>
	<title><![CDATA[Bioinformatician stuck in wet-lab]]></title>
	<description><![CDATA[<p>This guide is aimed at pet bioinformaticians, and is meant to guide them towards better career development.</p>
<p><strong>1. Make friends with local bioinformatics groups</strong><br> <strong>2. Talk to your computing group</strong><br> <strong>3. Obtain clear expectations</strong><br> <strong>4. Rewrite your job description</strong><br> <strong>5. Papers</strong><br> <strong>6. Attend bioinformatics meetings</strong><br> <strong>7. Try first, ask later</strong></p><p>Address of the bookmark: <a href="http://biomickwatson.wordpress.com/2013/04/23/a-guide-for-the-lonely-bioinformatician/" rel="nofollow">http://biomickwatson.wordpress.com/2013/04/23/a-guide-for-the-lonely-bioinformatician/</a></p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38561/hawkeye-an-interactive-visual-analytics-tool-for-genome-assemblies</guid>
	<pubDate>Tue, 01 Jan 2019 11:56:17 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38561/hawkeye-an-interactive-visual-analytics-tool-for-genome-assemblies</link>
	<title><![CDATA[Hawkeye: an interactive visual analytics tool for genome assemblies]]></title>
	<description><![CDATA[<p><span>Genome sequencing remains an inexact science, and genome sequences can contain significant errors if they are not carefully examined. Hawkeye is our new visual analytics tool for genome assemblies, designed to aid in identifying and correcting assembly errors. Users can analyze all levels of an assembly along with summary statistics and assembly metrics, and are guided by a ranking component towards likely mis-assemblies. Hawkeye is freely available and released as part of the open source AMOS project&nbsp;</span><span><a href="http://amos.sourceforge.net/hawkeye"><span>http://amos.sourceforge.net/hawkeye</span></a></span><span>.</span></p>
<p>https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-3-r34</p><p>Address of the bookmark: <a href="http://amos.sourceforge.net/wiki/index.php?title=Hawkeye" rel="nofollow">http://amos.sourceforge.net/wiki/index.php?title=Hawkeye</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
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