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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/31526?offset=1030</link>
	<atom:link href="https://bioinformaticsonline.com/related/31526?offset=1030" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/37198/understanding-blastn-output-format-6</guid>
	<pubDate>Wed, 27 Jun 2018 18:38:21 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/37198/understanding-blastn-output-format-6</link>
	<title><![CDATA[Understanding BLASTn output format 6 !]]></title>
	<description><![CDATA[<h3 id="sites-page-title-header" style="text-align: left;"><span>BLASTn output format 6</span></h3><div id="sites-canvas-main"><div id="sites-canvas-main-content"><div dir="ltr"><div><div><em>BLASTn</em> maps DNA against DNA, for example gene sequences against a reference genome<br /><br /><code><strong>blastn</strong>  -query <span>genes.ffn</span>  -subject <span>genome.fna</span>  -outfmt <strong>6</strong></code></div><h2>BLASTn tabular output format 6</h2>
<p><strong>Column headers:</strong><br /><code>qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore</code><br /></p>
<table border="1" cellspacing="0">
<tbody>
<tr>
<td> 1.</td>
<td> qseqid</td>
<td> query (e.g., gene) sequence id</td>
</tr>
<tr>
<td> 2.</td>
<td> sseqid</td>
<td> subject (e.g., reference genome) sequence id</td>
</tr>
<tr>
<td> 3.</td>
<td> pident</td>
<td> percentage of identical matches</td>
</tr>
<tr>
<td> 4.</td>
<td> length</td>
<td> alignment length</td>
</tr>
<tr>
<td> 5.</td>
<td> mismatch</td>
<td> number of mismatches</td>
</tr>
<tr>
<td> 6.</td>
<td> gapopen</td>
<td> number of gap openings</td>
</tr>
<tr>
<td> 7.</td>
<td> qstart</td>
<td> start of alignment in query</td>
</tr>
<tr>
<td> 8.</td>
<td> qend</td>
<td> end of alignment in query</td>
</tr>
<tr>
<td> 9.</td>
<td> sstart</td>
<td> start of alignment in subject</td>
</tr>
<tr>
<td> 10.</td>
<td> send</td>
<td> end of alignment in subject</td>
</tr>
<tr>
<td> 11.</td>
<td> evalue</td>
<td> <a href="http://www.metagenomics.wiki/tools/blast/evalue">expect value</a></td>
</tr>
<tr>
<td> 12.</td>
<td> bitscore</td>
<td> <a href="http://www.metagenomics.wiki/tools/blast/evalue"><strong>bit score</strong></a></td>
</tr>
</tbody>
</table>
<p><strong><br /></strong></p>
</div><h2><a name="TOC-Define-your-own-output-format" id="TOC-Define-your-own-output-format"></a>Define your own output format</h2><div><em>by adding the option -outfmt, as for example: </em><strong><br /></strong></div>
<p><code><strong>-outfmt</strong> <strong>"6</strong> <span>qseqid sseqid pident qlen length mismatch gapope evalue bitscore</span><strong>"</strong></code><br /><br /><em><strong>supported format specifiers are:</strong></em><br /><code>qseqid    </code>Query Seq-id<br /><code>qgi       </code>Query GI<br /><code>qacc      </code>Query accesion<br /><code>qaccver   </code>Query accesion.version<br /><code>qlen      </code>Query sequence length<br /><code>sseqid    </code>Subject Seq-id<br /><code>sallseqid </code>All subject Seq-id(s), separated by a ';'<br /><code>sgi       </code>Subject GI<br /><code>sallgi    </code>All subject GIs<br /><code>sacc      </code>Subject accession<br /><code>saccver   </code>Subject accession.version<br /><code>sallacc   </code>All subject accessions<br /><code>slen      </code>Subject sequence length<br /><code>qstart    </code>Start of alignment in query<br /><code>qend      </code>End of alignment in query<br /><code>sstart    </code>Start of alignment in subject<br /><code>send      </code>End of alignment in subject<br /><code>qseq      </code>Aligned part of query sequence<br /><code>sseq      </code>Aligned part of subject sequence<br /><code>evalue    </code>Expect value<br /><code>bitscore  </code>Bit score<br /><code>score     </code>Raw score<br /><code>length    </code>Alignment length<br /><code>pident    </code>Percentage of identical matches<br /><code>nident    </code>Number of identical matches<br /><code>mismatch  </code>Number of mismatches<br /><code>positive  </code>Number of positive-scoring matches<br /><code>gapopen   </code>Number of gap openings<br /><code>gaps      </code>Total number of gaps<br /><code>ppos      </code>Percentage of positive-scoring matches<br /><code>frames    </code>Query and subject frames separated by a '/'<br /><code>qframe    </code>Query frame<br /><code>sframe    </code>Subject frame<br /><code>btop      </code>Blast traceback operations (BTOP)<br /><code>staxids   </code>Subject Taxonomy ID(s), separated by a ';'<br /><code>sscinames </code>Subject Scientific Name(s), separated by a ';'<br /><code>scomnames </code>Subject Common Name(s), separated by a ';'<br /><code>sblastnames </code>Subject Blast Name(s), separated by a ';'   (in alphabetical order)<br /><code>sskingdoms  </code>Subject Super Kingdom(s), separated by a ';'     (in alphabetical order) <br /><code>stitle      </code>Subject Title<br /><code>salltitles  </code>All Subject Title(s), separated by a '&lt;&gt;'<br /><code>sstrand   </code>Subject Strand<br /><code>qcovs     </code>Query Coverage Per Subject<br /><code>qcovhsp   </code>Query Coverage Per HSP<br /><strong><br /><em>default values are:</em></strong><br /><code><code>-outfmt "</code>6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore"</code></p>
</div></div></div>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/24041/junior-bioinformatic-position</guid>
  <pubDate>Wed, 26 Aug 2015 05:35:28 -0500</pubDate>
  <link></link>
  <title><![CDATA[Junior Bioinformatic position]]></title>
  <description><![CDATA[
<p>Junior Bioinformatic position in the laboratory of Inflammation and immunology in cardiovascular pathologies at Humanitas:</p>

<p>We are seeking a highly motivated young PhD student with strong interest in high throughput data analysis.<br />Detailed descriptions of our recent research activities may be found here:<br />http://www.humanitas-research.org/condorelli-gianluigi-md-phd/</p>

<p>Position is available starting from October/November. A probationary period of one month will be required.<br /> <br />Please send a CV along with a cover letter stating the reasons for applying and contact details of one or more referees to Dr. Paolo Kunderfranco (paolo.kunderfranco@humanitasresearch.it).</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/43424/rest-api</guid>
	<pubDate>Mon, 04 Oct 2021 12:46:40 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/43424/rest-api</link>
	<title><![CDATA[REST API]]></title>
	<description><![CDATA[<h3 id="PSIBLASTHelpandDocumentation-RESTAPI">REST API</h3><p>The&nbsp;<a href="https://www.ebi.ac.uk/seqdb/confluence/pages/viewpage.action?pageId=68165098">Representational State Transfer (REST)</a>&nbsp;sample clients are provided for a number of programming languages. For details of how to use these clients,&nbsp;<a href="https://github.com/ebi-wp/webservice-clients">download</a>&nbsp;the client and run the program without any arguments.</p><div><table><colgroup><col><col><col></colgroup>
<thead>
<tr><th scope="col">
<div>Language</div>
</th><th scope="col">
<div>Download</div>
</th><th scope="col">
<div>Requirements</div>
</th></tr>
</thead>
<tbody>
<tr><th>Perl</th>
<td><a href="https://raw.githubusercontent.com/ebi-wp/webservice-clients/master/perl/psiblast.pl">psiblast.pl</a></td>
<td><a href="http://search.cpan.org/perldoc?LWP">LWP</a>&nbsp;and&nbsp;<a href="http://search.cpan.org/perldoc?XML::Simple">XML::Simple</a></td>
</tr>
<tr><th colspan="1">
<h4 id="PSIBLASTHelpandDocumentation-Python">Python</h4>
</th>
<td colspan="1">
<p><a href="https://raw.githubusercontent.com/ebi-wp/webservice-clients/master/python/psiblast.py">psiblast.py</a></p>
</td>
<td colspan="1"><a href="https://pypi.python.org/pypi/xmltramp2/3.0.10" title="https://pypi.python.org/pypi/xmltramp2/3.0.10">xmltramp2</a></td>
</tr>
</tbody>
</table></div><p>For details see&nbsp;<a href="https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/Environment+setup+for+REST+Web+Services">Environment setup for REST Web Services</a>&nbsp;and&nbsp;<a href="https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/Examples+for+Perl+REST+Web+Services+Clients">Examples for Perl REST Web Services Clients</a>&nbsp;pages.</p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/6268/project-fellow-national-institute-of-malaria-research</guid>
  <pubDate>Tue, 12 Nov 2013 07:40:51 -0600</pubDate>
  <link></link>
  <title><![CDATA[Project Fellow @ National Institute of Malaria Research]]></title>
  <description><![CDATA[
<p>National Institute of Malaria Research</p>

<p>Sector 8, Dwarka, Delhi -110077</p>

<p>WALK IN INTERVIEW</p>

<p>One position of project fellow is to be filled up in a DRL- funded research project on Molecular and morphological characterization of An. fluviatilis in North-eastern states and bordering areas. The position is purely temporary for one year and can be extended</p>

<p>Essential qualifications</p>

<p>Master’s degree in any branch of Life Sciences with hands on experience in molecular biology and/or bioinformatics.</p>

<p>Age limit: 28 years, (relaxation for SC/ST/OBC candidates as per government of India rules)</p>

<p>Stipend: Rs.12, 000.00 per month (fixed)</p>

<p>Eligible candidates may walk in for an interview on 15 November 2013 at 11 AM at the above mentioned address along with a copy of CV (with a passport size photograph affixed), photocopies of all mark sheets/certificates and originals (for verifications). No TA/DA will be paid for attending the interview .Registration of candidates will start at 10:00AM and end at 10:45 AM.</p>

<p>Advertisement: http://www.mrcindia.org/vacancy/add-4.doc</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36893/beap-blast-extension-and-assembly-program</guid>
	<pubDate>Mon, 11 Jun 2018 04:52:56 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36893/beap-blast-extension-and-assembly-program</link>
	<title><![CDATA[BEAP: Blast Extension and Assembly Program]]></title>
	<description><![CDATA[The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide databases in an attempt to obtain all sequences that overlaps, directly or indirectly, with the "primer" therefore help to "extend" the length of the original sequence for constructing a "full length" sequence for functional analysis, or at least to obtain neighboring regions of the segment for SNP discovery and linkage disequilibrium analysis. The confidence of assembling the resulting sequences is achieved by using a known genome, such as human genome, as a reference.
 
https://www.animalgenome.org/tools/beap/<p>Address of the bookmark: <a href="https://www.animalgenome.org/tools/beap/" rel="nofollow">https://www.animalgenome.org/tools/beap/</a></p>]]></description>
	<dc:creator>Shruti Paniwala</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/6560/the-graveley-lab</guid>
  <pubDate>Tue, 19 Nov 2013 18:02:48 -0600</pubDate>
  <link></link>
  <title><![CDATA[The Graveley Lab]]></title>
  <description><![CDATA[
<p>Research in the Graveley lab is primarily focused on the regulation of alternative splicing and small RNA mediated gene regulation. These are fascinating and extraordinarily important mechanisms by which genes can be regulated. Our long-term goals are to understand how these processes are regulated at a mechanistic level and to understand the logic of these processes in significant biological settings. To achieve these goals, we strive to think outside the box to creatively attack the problems being addressed using a wide variety of approaches that include biochemistry, genetics, imaging, deep sequencing, large-scale RNAi screening and bioinformatics.</p>

<p>Lab page @ http://graveleylab.cam.uchc.edu/Graveley/index.html</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/7153/phd-student-in-computational-systems-biology</guid>
  <pubDate>Tue, 10 Dec 2013 18:46:05 -0600</pubDate>
  <link></link>
  <title><![CDATA[Ph.D. student in Computational Systems Biology]]></title>
  <description><![CDATA[
<p>Ph.D. student in Computational Systems Biology</p>

<p>Location : The Luxembourg Centre for Systems Biomedicine (LCSB) at the University of Luxembourg, Luxembourg, Luxembourg<br />Deadline for applications : unknown.<br />Description :</p>

<p>The Luxembourg Centre for Systems Biomedicine (LCSB) was created within the Health Technologies Initiative from the Government of Luxembourg as one of the research priorities of the University of Luxembourg. The LCSB is an Interdisciplinary Centre of the University that combines experimental and computational approaches to analyse complex biological systems and disease processes. The Computational Biology Group (CBG) provides the LCSB with a solid infrastructure in developing theoretical framework for computational modeling on biomedical problems, especially in the area of network biology in the context of cellular programming/reprogramming. The CBG group includes researchers with theoretical, computational and wet lab backgrounds, thereby providing an unusually interdisciplinary environment.<br />The Computational Biology Group seeks a highly-skilled Ph.D. student to work on an exciting project on reconstruction and analysis of an integrated gene regulatory network model to elucidate key mechanisms of cellular reprogramming. The model will rely on the integration and mining of diverse transcriptomics and epigenomics data of different cell types from the Central Nervous System. The Ph.D. student is expected to collaborate with other members of the CBG to develop a computational methodology aiming at designing, in-silico, cellular reprogramming events, with a focus on the nervous system. This project will be carried out in collaboration with Prof. Noel Buckleys lab at Kings College London.<br />Requirements of the ideal candidate:<br />Master degree in Bioinformatics, Computer Science, Biology or a related discipline<br />Prior experience in mathematical modelling of biological networks, especially in network inference and analysis<br />Excellent working knowledge in English.<br />.<br />We offer:<br />Full contract for Ph.D. student for three years with possibility of renewal<br />Opportunity to do applied research to medical problems within a highly dynamic research institution (LCSB) and in collaboration with internationally recognized partners<br />An exciting international environment<br />A very competitive salary</p>

<p>For further information, please contact:</p>

<p>Prof. Dr. Antonio del Sol<br />E-mail: antonio.delsol@uni.lu</p>

<p>Applications should contain the following documents:<br />A detailed curriculum vitae<br />cover letter mentioning the reference number<br />description of past research experience and future interests<br />name and addresses of three referees</p>

<p>All applications should be sent preferably in electronic version until December 31st, 2013 to the following address:</p>

<p>Luxembourg Centre for Systems Biomedicine (LCSB)<br />University of Luxembourg<br />7, avenue des Hauts-Fourneaux<br />L-4362 Esch-sur-Alzette<br />Tel: +352-466644-6982 (Office)<br />Email: antonio.delsol@uni.lu<br />http://www.lcsb.lu</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/6836/research-fellow-mendel-laboratory</guid>
  <pubDate>Tue, 26 Nov 2013 00:07:57 -0600</pubDate>
  <link></link>
  <title><![CDATA[Research Fellow @ Mendel laboratory]]></title>
  <description><![CDATA[
<p>IRCCS Casa Sollievo della Sofferenza – Mendel laboratory is seeking one talented bioinformatician (Rome)<br />Start date: immediate</p>

<p>Duration: 1 year</p>

<p>Funding Source: Institutional<br />Salary on grant: B2 (€ 22.000/year gross)<br />Contact Person (Referent): Tommaso Mazza<br />Ref. E-Mail: t.mazza@css-mendel.it<br />Tel: +39 06 44160526<br />Fax: +39 06 44160548</p>

<p>Job Description: The bioinformatics unit at IRCCS Casa Sollievo della Sofferenza - Mendel laboratory in Rome is looking for one young PhD bioinformatician with specific experience and/or interest in the analysis of transcriptomic data.</p>

<p>The candidate will be mainly in charge of developing research on a range of hot applications and projects, dealing with microarrays, RNA-Seq and miRNA-Seq data. Main activities will be: (i) data analysis (short-reads mapping, variants call and annotation, functional enrichment analysis of gene expression data); (ii) networks analysis and simulation (artificial knockout, redundancy and lethality analysis, gene set essentiality); (iii) developing of ad-hoc software solutions/routines on clusters of CPUs and GPUs.</p>

<p>The correct cultural background (training in Biology / Computer Science / Statistics or a mix of the three) and a strong interest in working with high throughput data analysis will be considered at the same level of specific experience in the above-mentioned fields.<br />Knowledge of molecular modeling and simulation and one of these languages: python, perl, R, Java, C++, C# is a golden plus. Good knowledge of Scientific English will be positively evaluated for this position, together with good presentation and teamwork skills.</p>

<p>A CV with one professional reference, details on educational background and of the biological and/or bioinformatic and/or data analysis skills and experience should be sent by email for a preliminary selection to: Tommaso Mazza, CSS-Mendel: t.mazza@css-mendel.it</p>

<p>Context<br />Casa Sollievo della Sofferenza is an Institute for hospitalization, care, and scientific research located in San Giovanni Rotondo, Italy. It integrates clinical assistance (with inpatient and outpatient facilities) and research. It has an affiliate institute, CSS-Mendel, located in Rome. Between the two sites, it employs over 100 researchers who focus on genetics. The Center is equipped with state of the art genomics technology (SOLiD 5500XL next generation sequencer, Illumina MiSeq, Affymetrix/Agilent microarray platforms, etc) as well as a dedicated high performance computing facility, a non-conventional workstation of GPUs and a short- and long-term storage disk.</p>

<p>Applications<br />Candidates should send:<br />• a cover letter explaining the role they would like to undertake within the Center, even if it is not listed in this job adv, stating clearly why they would be a good fit to the proposed role, and what they would bring to the Center in terms of expertise, ideas, talent;<br />• a CV including a list of publications;<br />• List of referees;</p>

<p>More at http://www.css-mendel.it/</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/7212/bioinformatics-group-at-boku-university</guid>
  <pubDate>Thu, 12 Dec 2013 17:53:10 -0600</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics group at Boku University]]></title>
  <description><![CDATA[
<p>The Bioinformatics group at Boku University has two main areas of interest, underpinning a common goal, the study of complex systems in living organisms. To overcome the engineered redundancies and combinatorial effects prevalent in higher eukaryotes, novel views augmenting the classical gene by gene approaches are required. We combine</p>

<p>1. Work to establish improved quantitative experimental assays (such as microarrays or differential in-gel electrophoresis) and<br />2. Development of modern computational methods (such as hierarchical probabilistic models or integration of heterogeneous data sources)</p>

<p>Lab page @ http://bioinf.boku.ac.at/</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/7216/free-math-books</guid>
	<pubDate>Thu, 12 Dec 2013 19:38:34 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/7216/free-math-books</link>
	<title><![CDATA[Free math books]]></title>
	<description><![CDATA[<p>Bioinformatics require some match skills, therefore I decided to provide this wonderful math eBooks links to the BOL community.</p>
<p>Please add ur links/bookmarks in comment section.</p><p>Address of the bookmark: <a href="http://physicsdatabase.com/free-math-books/" rel="nofollow">http://physicsdatabase.com/free-math-books/</a></p>]]></description>
	<dc:creator>Manisha Mishra</dc:creator>
</item>

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