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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/29029?offset=1280</link>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/20271/research-associate-tata-memorial-centre-advanced-centre-for-treatment-research-and-education-in-cancer-kharghar-navi-mumbai</guid>
  <pubDate>Thu, 08 Jan 2015 20:53:57 -0600</pubDate>
  <link></link>
  <title><![CDATA[Research Associate	@ TATA MEMORIAL CENTRE ADVANCED CENTRE FOR TREATMENT, RESEARCH AND EDUCATION IN CANCER KHARGHAR, NAVI MUMBAI]]></title>
  <description><![CDATA[
<p>TATA MEMORIAL CENTRE ADVANCED CENTRE FOR TREATMENT, RESEARCH AND EDUCATION IN CANCER KHARGHAR, NAVI MUMBAI – 410210</p>

<p>Website: www.actrec.gov.in; Ph: 27405000</p>

<p>No. ACTREC/Advt./ 66 /2014 23rd December, 2014<br />Research Associate	</p>

<p>International Cancer Genome Consortium (ICGC) - India Project (IRB Project No. 3 A/c. No. 2408)</p>

<p>Dr. Rajiv Sarin</p>

<p>Duration of the Project: One year Extendable up to Three years.</p>

<p>Consolidated Salary: Rs. 42,000/- p.m.</p>

<p>Application last date: 8th January, 2015.</p>

<p>Interview Date &amp; Time: 21st January, 2015, at 11.00 a.m.</p>

<p>Venue: Conference Room, 3rd floor, Khanolkar Shodhika, ACTREC.</p>

<p>Essential Qualifications and Experience:</p>

<p>Ph.D (any branch of Life Sciences)</p>

<p>The candidate must have at least one year experience after Ph.D., preferably in Genomics and Molecular Biology.</p>

<p>Candidates fulfilling these requirements should pre register themselves by sending their application in the prescribed format with recent CV and contact details of 2 referees by e-mail to icgc@actrec.gov.in latest 8th January, 2015 by 10.00 a.m.</p>

<p>Candidates shortlisted for the interview will be intimated by email on or before 9th January, 2015.</p>

<p>The interviews would be held on 21st January 2015 and will be only for the pre registered candidates who have been shortlisted.<br />No T.A./D.A. will be admissible for attending the interview.</p>

<p>At the time of Interview the candidate should bring original certificates along with CV with contact details of 2 referees and submit the photocopies (attested) of the certificates, with a recent passport size photograph.</p>

<p>Advertisement: www.actrec.gov.in/data%20files/2014/Walk-in-Research-Fellow-26-12-14.doc</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44865/snp-analysis-unlocking-the-secrets-in-our-dna</guid>
	<pubDate>Wed, 16 Jul 2025 01:31:45 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44865/snp-analysis-unlocking-the-secrets-in-our-dna</link>
	<title><![CDATA[SNP Analysis: Unlocking the Secrets in Our DNA]]></title>
	<description><![CDATA[<p>Single Nucleotide Polymorphisms (SNPs) are the most common type of genetic variation in humans&mdash;and many other organisms. A single base change in the DNA sequence (for example, an A instead of a G) can influence everything from our eye color to our risk of developing diseases. Analyzing these tiny changes has become central to modern genetics, medicine, agriculture, and evolutionary biology.</p><p><strong>What are SNPs?</strong><br />SNPs (pronounced "snips") are positions in the genome where individuals differ by a single nucleotide. For example:</p><p>Reference: ...A T G C A T G A...<br />Variant:&nbsp; &nbsp; &nbsp;...A T G T A T G A...</p><p>Here, the C in the reference genome has been replaced by a T in the variant.</p><p>SNPs occur roughly every 300&ndash;1,000 bases in the human genome, meaning there are millions of them scattered throughout our DNA. Most SNPs have no effect on health, but some are linked to disease susceptibility, drug response, and other traits.</p><p><strong>Why Do We Analyze SNPs?</strong><br />1. Medical Genetics</p><p>Identify disease-associated variants (e.g., BRCA1/2 in breast cancer).</p><p>Predict drug response (pharmacogenomics).</p><p>Enable precision medicine by tailoring treatments.</p><p>2. Population Genetics &amp; Ancestry</p><p>Trace human migration and ancestry.</p><p>Study genetic diversity within and between populations.</p><p>3. Agriculture &amp; Animal Breeding</p><p>Select for desirable traits (drought resistance, yield, disease resistance).</p><p>Improve breeding efficiency in livestock.</p><p>4. Evolutionary Biology</p><p>Track natural selection.</p><p>Study adaptation in wild populations.</p><p><strong>How is SNP Analysis Performed?</strong><br />SNP analysis can be broadly divided into three steps:</p><p>SNP Detection<br />Genotyping arrays: Chips that test hundreds of thousands of known SNP positions simultaneously. Fast and affordable, widely used in consumer ancestry testing.</p><p>Whole-genome or whole-exome sequencing: Can detect known and novel SNPs across the genome.</p><p>Targeted sequencing or PCR: For focused analysis of specific regions.</p><p>Variant Calling<br />Sequencing data is aligned to a reference genome. Bioinformatics tools (e.g., GATK, bcftools) identify positions where the sequenced sample differs from the reference.</p><p>Annotation and Interpretation<br />Tools (e.g., SnpEff, VEP) predict the functional impact of SNPs.</p><p>Are the SNPs in coding regions? Do they cause amino acid changes? Are they known to be pathogenic?</p><p>Databases like dbSNP, ClinVar, and GWAS Catalog provide information on known associations.</p><p>Common Tools for SNP Analysis<br />Alignment: BWA, Bowtie2</p><p>Variant Calling: GATK, FreeBayes</p><p>Visualization: IGV, UCSC Genome Browser</p><p>Annotation: SnpEff, VEP</p><p>Statistical Analysis: PLINK, SNPTEST</p><p><strong>Challenges in SNP Analysis</strong><br />False positives/negatives: Sequencing errors, alignment issues.</p><p>Population stratification: Confounding in association studies.</p><p>Interpretation: Many SNPs have unknown or complex effects.</p><p>Researchers address these with rigorous quality control, large datasets, and increasingly sophisticated statistical models.</p><p><strong>The Future of SNP Analysis</strong><br />With advances in sequencing technology and AI-driven analysis, SNP studies are expanding:</p><p>Polygenic risk scores predict disease risk based on thousands of SNPs.</p><p>Large-scale biobanks (e.g., UK Biobank, All of Us) enable powerful genome-wide association studies (GWAS).</p><p>CRISPR and functional assays help validate SNP effects in the lab.</p><p>SNP analysis is at the heart of the genomic revolution, promising insights into biology, health, and evolution at unprecedented scale.</p><p><strong>Conclusion</strong><br />From diagnosing rare diseases to designing better crops, SNP analysis is a foundational tool in modern science. As our ability to sequence and interpret genomes improves, so will our understanding of these tiny&mdash;but mighty&mdash;variations in DNA.</p><p>&nbsp;</p>]]></description>
	<dc:creator>Abhi</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/20454/comparative-genomics-in-ensembl</guid>
	<pubDate>Wed, 21 Jan 2015 08:31:11 -0600</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/20454/comparative-genomics-in-ensembl</link>
	<title><![CDATA[Comparative Genomics in Ensembl]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/dDRdCnZOMCM" frameborder="0" allowfullscreen></iframe>The Ensembl browser provides viewable whole-genome alignments, homologues and phylogenetic gene trees, protein families, and ancestral sequences.  Learn how to view and export these data in this video.]]></description>
	
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/39307/awk-for-beginners</guid>
	<pubDate>Fri, 26 Apr 2019 16:19:41 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/39307/awk-for-beginners</link>
	<title><![CDATA[AWK for beginners !]]></title>
	<description><![CDATA[<p>AWK is a standard tool on every POSIX-compliant UNIX system. It&rsquo;s like flex/lex, from the command-line, perfect for text-processing tasks and other scripting needs. It has a C-like syntax, but without mandatory semicolons (although, you should use them anyway, because they are required when you&rsquo;re writing one-liners, something AWK excels at), manual memory management, or static typing. It excels at text processing. You can call to it from a shell script, or you can use it as a stand-alone scripting language.</p><p>Why use AWK instead of Perl? Readability. AWK is easier to read than Perl. For simple text-processing scripts, particularly ones that read files line by line and split on delimiters, AWK is probably the right tool for the job.</p><div><pre><span>#!/usr/bin/awk -f</span>

<span># Comments are like this</span>


<span># AWK programs consist of a collection of patterns and actions.</span>
<span>pattern1</span> <span>{</span> <span>action</span><span>;</span> <span>}</span> <span># just like lex</span>
<span>pattern2</span> <span>{</span> <span>action</span><span>;</span> <span>}</span>

<span># There is an implied loop and AWK automatically reads and parses each</span>
<span># record of each file supplied. Each record is split by the FS delimiter,</span>
<span># which defaults to white-space (multiple spaces,tabs count as one)</span>
<span># You can assign FS either on the command line (-F C) or in your BEGIN</span>
<span># pattern</span>

<span># One of the special patterns is BEGIN. The BEGIN pattern is true</span>
<span># BEFORE any of the files are read. The END pattern is true after</span>
<span># an End-of-file from the last file (or standard-in if no files specified)</span>
<span># There is also an output field separator (OFS) that you can assign, which</span>
<span># defaults to a single space</span>

<span>BEGIN</span> <span>{</span>

    <span># BEGIN will run at the beginning of the program. It's where you put all</span>
    <span># the preliminary set-up code, before you process any text files. If you</span>
    <span># have no text files, then think of BEGIN as the main entry point.</span>

    <span># Variables are global. Just set them or use them, no need to declare..</span>
    <span>count</span> <span>=</span> <span>0</span><span>;</span>

    <span># Operators just like in C and friends</span>
    <span>a</span> <span>=</span> <span>count</span> <span>+</span> <span>1</span><span>;</span>
    <span>b</span> <span>=</span> <span>count</span> <span>-</span> <span>1</span><span>;</span>
    <span>c</span> <span>=</span> <span>count</span> <span>*</span> <span>1</span><span>;</span>
    <span>d</span> <span>=</span> <span>count</span> <span>/</span> <span>1</span><span>;</span> <span># integer division</span>
    <span>e</span> <span>=</span> <span>count</span> <span>%</span> <span>1</span><span>;</span> <span># modulus</span>
    <span>f</span> <span>=</span> <span>count</span> <span>^</span> <span>1</span><span>;</span> <span># exponentiation</span>

    <span>a</span> <span>+=</span> <span>1</span><span>;</span>
    <span>b</span> <span>-=</span> <span>1</span><span>;</span>
    <span>c</span> <span>*=</span> <span>1</span><span>;</span>
    <span>d</span> <span>/=</span> <span>1</span><span>;</span>
    <span>e</span> <span>%=</span> <span>1</span><span>;</span>
    <span>f</span> <span>^=</span> <span>1</span><span>;</span>

    <span># Incrementing and decrementing by one</span>
    <span>a</span><span>++</span><span>;</span>
    <span>b</span><span>--</span><span>;</span>

    <span># As a prefix operator, it returns the incremented value</span>
    <span>++</span><span>a</span><span>;</span>
    <span>--</span><span>b</span><span>;</span>

    <span># Notice, also, no punctuation such as semicolons to terminate statements</span>

    <span># Control statements</span>
    <span>if</span> <span>(</span><span>count</span> <span>==</span> <span>0</span><span>)</span>
        <span>print</span> <span>"Starting with count of 0"</span><span>;</span>
    <span>else</span>
        <span>print</span> <span>"Huh?"</span><span>;</span>

    <span># Or you could use the ternary operator</span>
    <span>print</span> <span>(</span><span>count</span> <span>==</span> <span>0</span><span>)</span> <span>?</span> <span>"Starting with count of 0"</span> <span>:</span> <span>"Huh?"</span><span>;</span>

    <span># Blocks consisting of multiple lines use braces</span>
    <span>while</span> <span>(</span><span>a</span> <span>&lt;</span> <span>10</span><span>)</span> <span>{</span>
        <span>print</span> <span>"String concatenation is done"</span> <span>" with a series"</span> <span>" of"</span>
            <span>" space-separated strings"</span><span>;</span>
        <span>print</span> <span>a</span><span>;</span>

        <span>a</span><span>++</span><span>;</span>
    <span>}</span>

    <span>for</span> <span>(</span><span>i</span> <span>=</span> <span>0</span><span>;</span> <span>i</span> <span>&lt;</span> <span>10</span><span>;</span> <span>i</span><span>++</span><span>)</span>
        <span>print</span> <span>"Good ol' for loop"</span><span>;</span>

    <span># As for comparisons, they're the standards:</span>
    <span># a &lt; b   # Less than</span>
    <span># a &lt;= b  # Less than or equal</span>
    <span># a != b  # Not equal</span>
    <span># a == b  # Equal</span>
    <span># a &gt; b   # Greater than</span>
    <span># a &gt;= b  # Greater than or equal</span>

    <span># Logical operators as well</span>
    <span># a &amp;&amp; b  # AND</span>
    <span># a || b  # OR</span>

    <span># In addition, there's the super useful regular expression match</span>
    <span>if</span> <span>(</span><span>"foo"</span> <span>~</span> <span>"^fo+$"</span><span>)</span>
        <span>print</span> <span>"Fooey!"</span><span>;</span>
    <span>if</span> <span>(</span><span>"boo"</span> <span>!~</span> <span>"^fo+$"</span><span>)</span>
        <span>print</span> <span>"Boo!"</span><span>;</span>

    <span># Arrays</span>
    <span>arr</span><span>[</span><span>0</span><span>]</span> <span>=</span> <span>"foo"</span><span>;</span>
    <span>arr</span><span>[</span><span>1</span><span>]</span> <span>=</span> <span>"bar"</span><span>;</span>

    <span># You can also initialize an array with the built-in function split()</span>

    <span>n</span> <span>=</span> <span>split</span><span>(</span><span>"foo:bar:baz"</span><span>,</span> <span>arr</span><span>,</span> <span>":"</span><span>);</span>

    <span># You also have associative arrays (actually, they're all associative arrays)</span>
    <span>assoc</span><span>[</span><span>"foo"</span><span>]</span> <span>=</span> <span>"bar"</span><span>;</span>
    <span>assoc</span><span>[</span><span>"bar"</span><span>]</span> <span>=</span> <span>"baz"</span><span>;</span>

    <span># And multi-dimensional arrays, with some limitations I won't mention here</span>
    <span>multidim</span><span>[</span><span>0</span><span>,</span><span>0</span><span>]</span> <span>=</span> <span>"foo"</span><span>;</span>
    <span>multidim</span><span>[</span><span>0</span><span>,</span><span>1</span><span>]</span> <span>=</span> <span>"bar"</span><span>;</span>
    <span>multidim</span><span>[</span><span>1</span><span>,</span><span>0</span><span>]</span> <span>=</span> <span>"baz"</span><span>;</span>
    <span>multidim</span><span>[</span><span>1</span><span>,</span><span>1</span><span>]</span> <span>=</span> <span>"boo"</span><span>;</span>

    <span># You can test for array membership</span>
    <span>if</span> <span>(</span><span>"foo"</span> <span>in</span> <span>assoc</span><span>)</span>
        <span>print</span> <span>"Fooey!"</span><span>;</span>

    <span># You can also use the 'in' operator to traverse the keys of an array</span>
    <span>for</span> <span>(</span><span>key</span> <span>in</span> <span>assoc</span><span>)</span>
        <span>print</span> <span>assoc</span><span>[</span><span>key</span><span>];</span>

    <span># The command line is in a special array called ARGV</span>
    <span>for</span> <span>(</span><span>argnum</span> <span>in</span> <span>ARGV</span><span>)</span>
        <span>print</span> <span>ARGV</span><span>[</span><span>argnum</span><span>];</span>

    <span># You can remove elements of an array</span>
    <span># This is particularly useful to prevent AWK from assuming the arguments</span>
    <span># are files for it to process</span>
    <span>delete</span> <span>ARGV</span><span>[</span><span>1</span><span>];</span>

    <span># The number of command line arguments is in a variable called ARGC</span>
    <span>print</span> <span>ARGC</span><span>;</span>

    <span># AWK has several built-in functions. They fall into three categories. I'll</span>
    <span># demonstrate each of them in their own functions, defined later.</span>

    <span>return_value</span> <span>=</span> <span>arithmetic_functions</span><span>(</span><span>a</span><span>,</span> <span>b</span><span>,</span> <span>c</span><span>);</span>
    <span>string_functions</span><span>();</span>
    <span>io_functions</span><span>();</span>
<span>}</span>

<span># Here's how you define a function</span>
<span>function</span> <span>arithmetic_functions</span><span>(</span><span>a</span><span>,</span> <span>b</span><span>,</span> <span>c</span><span>,</span>     <span>d</span><span>)</span> <span>{</span>

    <span># Probably the most annoying part of AWK is that there are no local</span>
    <span># variables. Everything is global. For short scripts, this is fine, even</span>
    <span># useful, but for longer scripts, this can be a problem.</span>

    <span># There is a work-around (ahem, hack). Function arguments are local to the</span>
    <span># function, and AWK allows you to define more function arguments than it</span>
    <span># needs. So just stick local variable in the function declaration, like I</span>
    <span># did above. As a convention, stick in some extra whitespace to distinguish</span>
    <span># between actual function parameters and local variables. In this example,</span>
    <span># a, b, and c are actual parameters, while d is merely a local variable.</span>

    <span># Now, to demonstrate the arithmetic functions</span>

    <span># Most AWK implementations have some standard trig functions</span>
    <span>localvar</span> <span>=</span> <span>sin</span><span>(</span><span>a</span><span>);</span>
    <span>localvar</span> <span>=</span> <span>cos</span><span>(</span><span>a</span><span>);</span>
    <span>localvar</span> <span>=</span> <span>atan2</span><span>(</span><span>b</span><span>,</span> <span>a</span><span>);</span> <span># arc tangent of b / a</span>

    <span># And logarithmic stuff</span>
    <span>localvar</span> <span>=</span> <span>exp</span><span>(</span><span>a</span><span>);</span>
    <span>localvar</span> <span>=</span> <span>log</span><span>(</span><span>a</span><span>);</span>

    <span># Square root</span>
    <span>localvar</span> <span>=</span> <span>sqrt</span><span>(</span><span>a</span><span>);</span>

    <span># Truncate floating point to integer</span>
    <span>localvar</span> <span>=</span> <span>int</span><span>(</span><span>5.34</span><span>);</span> <span># localvar =&gt; 5</span>

    <span># Random numbers</span>
    <span>srand</span><span>();</span> <span># Supply a seed as an argument. By default, it uses the time of day</span>
    <span>localvar</span> <span>=</span> <span>rand</span><span>();</span> <span># Random number between 0 and 1.</span>

    <span># Here's how to return a value</span>
    <span>return</span> <span>localvar</span><span>;</span>
<span>}</span>

<span>function</span> <span>string_functions</span><span>(</span>    <span>localvar</span><span>,</span> <span>arr</span><span>)</span> <span>{</span>

    <span># AWK, being a string-processing language, has several string-related</span>
    <span># functions, many of which rely heavily on regular expressions.</span>

    <span># Search and replace, first instance (sub) or all instances (gsub)</span>
    <span># Both return number of matches replaced</span>
    <span>localvar</span> <span>=</span> <span>"fooooobar"</span><span>;</span>
    <span>sub</span><span>(</span><span>"fo+"</span><span>,</span> <span>"Meet me at the "</span><span>,</span> <span>localvar</span><span>);</span> <span># localvar =&gt; "Meet me at the bar"</span>
    <span>gsub</span><span>(</span><span>"e+"</span><span>,</span> <span>"."</span><span>,</span> <span>localvar</span><span>);</span> <span># localvar =&gt; "m..t m. at th. bar"</span>

    <span># Search for a string that matches a regular expression</span>
    <span># index() does the same thing, but doesn't allow a regular expression</span>
    <span>match</span><span>(</span><span>localvar</span><span>,</span> <span>"t"</span><span>);</span> <span># =&gt; 4, since the 't' is the fourth character</span>

    <span># Split on a delimiter</span>
    <span>n</span> <span>=</span> <span>split</span><span>(</span><span>"foo-bar-baz"</span><span>,</span> <span>arr</span><span>,</span> <span>"-"</span><span>);</span> <span># a[1] = "foo"; a[2] = "bar"; a[3] = "baz"; n = 3</span>

    <span># Other useful stuff</span>
    <span>sprintf</span><span>(</span><span>"%s %d %d %d"</span><span>,</span> <span>"Testing"</span><span>,</span> <span>1</span><span>,</span> <span>2</span><span>,</span> <span>3</span><span>);</span> <span># =&gt; "Testing 1 2 3"</span>
    <span>substr</span><span>(</span><span>"foobar"</span><span>,</span> <span>2</span><span>,</span> <span>3</span><span>);</span> <span># =&gt; "oob"</span>
    <span>substr</span><span>(</span><span>"foobar"</span><span>,</span> <span>4</span><span>);</span> <span># =&gt; "bar"</span>
    <span>length</span><span>(</span><span>"foo"</span><span>);</span> <span># =&gt; 3</span>
    <span>tolower</span><span>(</span><span>"FOO"</span><span>);</span> <span># =&gt; "foo"</span>
    <span>toupper</span><span>(</span><span>"foo"</span><span>);</span> <span># =&gt; "FOO"</span>
<span>}</span>

<span>function</span> <span>io_functions</span><span>(</span>    <span>localvar</span><span>)</span> <span>{</span>

    <span># You've already seen print</span>
    <span>print</span> <span>"Hello world"</span><span>;</span>

    <span># There's also printf</span>
    <span>printf</span><span>(</span><span>"%s %d %d %d\n"</span><span>,</span> <span>"Testing"</span><span>,</span> <span>1</span><span>,</span> <span>2</span><span>,</span> <span>3</span><span>);</span>

    <span># AWK doesn't have file handles, per se. It will automatically open a file</span>
    <span># handle for you when you use something that needs one. The string you used</span>
    <span># for this can be treated as a file handle, for purposes of I/O. This makes</span>
    <span># it feel sort of like shell scripting, but to get the same output, the string</span>
    <span># must match exactly, so use a variable:</span>

    <span>outfile</span> <span>=</span> <span>"/tmp/foobar.txt"</span><span>;</span>

    <span>print</span> <span>"foobar"</span> <span>&gt;</span> <span>outfile</span><span>;</span>

    <span># Now the string outfile is a file handle. You can close it:</span>
    <span>close</span><span>(</span><span>outfile</span><span>);</span>

    <span># Here's how you run something in the shell</span>
    <span>system</span><span>(</span><span>"echo foobar"</span><span>);</span> <span># =&gt; prints foobar</span>

    <span># Reads a line from standard input and stores in localvar</span>
    <span>getline</span> <span>localvar</span><span>;</span>

    <span># Reads a line from a pipe (again, use a string so you close it properly)</span>
    <span>cmd</span> <span>=</span> <span>"echo foobar"</span><span>;</span>
    <span>cmd</span> <span>|</span> <span>getline</span> <span>localvar</span><span>;</span> <span># localvar =&gt; "foobar"</span>
    <span>close</span><span>(</span><span>cmd</span><span>);</span>

    <span># Reads a line from a file and stores in localvar</span>
    <span>infile</span> <span>=</span> <span>"/tmp/foobar.txt"</span><span>;</span>
    <span>getline</span> <span>localvar</span> <span>&lt;</span> <span>infile</span><span>;</span> 
    <span>close</span><span>(</span><span>infile</span><span>);</span>
<span>}</span>

<span># As I said at the beginning, AWK programs consist of a collection of patterns</span>
<span># and actions. You've already seen the BEGIN pattern. Other</span>
<span># patterns are used only if you're processing lines from files or standard</span>
<span># input.</span>
<span>#</span>
<span># When you pass arguments to AWK, they are treated as file names to process.</span>
<span># It will process them all, in order. Think of it like an implicit for loop,</span>
<span># iterating over the lines in these files. these patterns and actions are like</span>
<span># switch statements inside the loop. </span>

<span>/^fo+bar$/</span> <span>{</span>

    <span># This action will execute for every line that matches the regular</span>
    <span># expression, /^fo+bar$/, and will be skipped for any line that fails to</span>
    <span># match it. Let's just print the line:</span>

    <span>print</span><span>;</span>

    <span># Whoa, no argument! That's because print has a default argument: $0.</span>
    <span># $0 is the name of the current line being processed. It is created</span>
    <span># automatically for you.</span>

    <span># You can probably guess there are other $ variables. Every line is</span>
    <span># implicitly split before every action is called, much like the shell</span>
    <span># does. And, like the shell, each field can be access with a dollar sign</span>

    <span># This will print the second and fourth fields in the line</span>
    <span>print</span> <span>$</span><span>2</span><span>,</span> <span>$</span><span>4</span><span>;</span>

    <span># AWK automatically defines many other variables to help you inspect and</span>
    <span># process each line. The most important one is NF</span>

    <span># Prints the number of fields on this line</span>
    <span>print</span> <span>NF</span><span>;</span>

    <span># Print the last field on this line</span>
    <span>print</span> <span>$</span><span>NF</span><span>;</span>
<span>}</span>

<span># Every pattern is actually a true/false test. The regular expression in the</span>
<span># last pattern is also a true/false test, but part of it was hidden. If you</span>
<span># don't give it a string to test, it will assume $0, the line that it's</span>
<span># currently processing. Thus, the complete version of it is this:</span>

<span>$</span><span>0</span> <span>~</span> <span>/^fo+bar$/</span> <span>{</span>
    <span>print</span> <span>"Equivalent to the last pattern"</span><span>;</span>
<span>}</span>

<span>a</span> <span>&gt;</span> <span>0</span> <span>{</span>
    <span># This will execute once for each line, as long as a is positive</span>
<span>}</span>

<span># You get the idea. Processing text files, reading in a line at a time, and</span>
<span># doing something with it, particularly splitting on a delimiter, is so common</span>
<span># in UNIX that AWK is a scripting language that does all of it for you, without</span>
<span># you needing to ask. All you have to do is write the patterns and actions</span>
<span># based on what you expect of the input, and what you want to do with it.</span>

<span># Here's a quick example of a simple script, the sort of thing AWK is perfect</span>
<span># for. It will read a name from standard input and then will print the average</span>
<span># age of everyone with that first name. Let's say you supply as an argument the</span>
<span># name of a this data file:</span>
<span>#</span>
<span># Bob Jones 32</span>
<span># Jane Doe 22</span>
<span># Steve Stevens 83</span>
<span># Bob Smith 29</span>
<span># Bob Barker 72</span>
<span>#</span>
<span># Here's the script:</span>

<span>BEGIN</span> <span>{</span>

    <span># First, ask the user for the name</span>
    <span>print</span> <span>"What name would you like the average age for?"</span><span>;</span>

    <span># Get a line from standard input, not from files on the command line</span>
    <span>getline</span> <span>name</span> <span>&lt;</span> <span>"/dev/stdin"</span><span>;</span>
<span>}</span>

<span># Now, match every line whose first field is the given name</span>
<span>$</span><span>1</span> <span>==</span> <span>name</span> <span>{</span>

    <span># Inside here, we have access to a number of useful variables, already</span>
    <span># pre-loaded for us:</span>
    <span># $0 is the entire line</span>
    <span># $3 is the third field, the age, which is what we're interested in here</span>
    <span># NF is the number of fields, which should be 3</span>
    <span># NR is the number of records (lines) seen so far</span>
    <span># FILENAME is the name of the file being processed</span>
    <span># FS is the field separator being used, which is " " here</span>
    <span># ...etc. There are plenty more, documented in the man page.</span>

    <span># Keep track of a running total and how many lines matched</span>
    <span>sum</span> <span>+=</span> <span>$</span><span>3</span><span>;</span>
    <span>nlines</span><span>++</span><span>;</span>
<span>}</span>

<span># Another special pattern is called END. It will run after processing all the</span>
<span># text files. Unlike BEGIN, it will only run if you've given it input to</span>
<span># process. It will run after all the files have been read and processed</span>
<span># according to the rules and actions you've provided. The purpose of it is</span>
<span># usually to output some kind of final report, or do something with the</span>
<span># aggregate of the data you've accumulated over the course of the script.</span>

<span>END</span> <span>{</span>
    <span>if</span> <span>(</span><span>nlines</span><span>)</span>
        <span>print</span> <span>"The average age for "</span> <span>name</span> <span>" is "</span> <span>sum</span> <span>/</span> <span>nlines</span><span>;</span>
<span>}</span>
</pre><p><span>&nbsp;</span></p></div>]]></description>
	<dc:creator>BioJoker</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/20471/bioinformatics-scripts</guid>
	<pubDate>Thu, 22 Jan 2015 22:29:39 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/20471/bioinformatics-scripts</link>
	<title><![CDATA[Bioinformatics Scripts]]></title>
	<description><![CDATA[<p>Some of the useful bioinformatics scripts.</p>
<p>For example ... contig-stats.pl is a Perl script that will automatically describe features of a sequence assembly.</p>
<p>http://milkweedgenome.org/?q=scripts</p><p>Address of the bookmark: <a href="http://milkweedgenome.org/?q=scripts" rel="nofollow">http://milkweedgenome.org/?q=scripts</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/20504/chromevol</guid>
	<pubDate>Sun, 25 Jan 2015 00:33:11 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/20504/chromevol</link>
	<title><![CDATA[ChromEvol]]></title>
	<description><![CDATA[<p>Chromosome number is a remarkably dynamic feature of eukaryotic evolution. Chromosome numbers can change by a duplication of the whole genome (a process termed polyploidy), or by single chromosome changes (ascending dysploidy via, e.g., chromosome fission or descending dysploidy via, e.g., chromosome fusion).<br> Of the various mechanisms of chromosome number change, polyploidy has received significant attention because of the impact such an event may have on the organism.<br> ChromEvol implements a series of likelihood models for the evolution of chromosome numbers. By comparing the fit of the different models to biological data, it may be possible to gain insight regarding the pathways by which the evolution of chromosome number proceeds. For each model, the program estimates the rates for the possible transitions assumed by the model, infers the set of ancestral chromosome numbers, and estimates the location along the tree for which polyploidy events (and other chromosome number changes) occurred. For further methodological details, see the publications and manual on the Downloads page.</p>
<p>http://www.tau.ac.il/~itaymay/cp/chromEvol/about.html</p><p>Address of the bookmark: <a href="http://www.tau.ac.il/~itaymay/cp/chromEvol/downloads.html" rel="nofollow">http://www.tau.ac.il/~itaymay/cp/chromEvol/downloads.html</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/20672/jrfra-structuralcomputational-biology-at-icgeb</guid>
  <pubDate>Thu, 29 Jan 2015 11:52:40 -0600</pubDate>
  <link></link>
  <title><![CDATA[JRF/RA Structural/Computational Biology at ICGEB]]></title>
  <description><![CDATA[
<p>Research Associate and JRF positions in the Structural and Computational Biology Group starting 1st March 2015. Collaborative projects include work on:</p>

<p>a) bioinformatics, systems and computational biology <br />b) malaria <br />c) drug discovery <br />d) genomics <br />e) microbiology <br />f) metabolic disorders <br />g) molecular medicine</p>

<p>Eligibility: Applicants must have one of the following :</p>

<p>1) INSPIRE award for undertakig either PhD or Postdoctoral research; <br />2) SPM award for PhD; <br />3) JRF for pursuing PhD from CSIR/DBT/ICMR</p>

<p>Interest and experience in Biochemistry/Bioinformatics/Biophysics/ Chemistry/Genomics/Molecular Biology/ is essential.</p>

<p>Submit curriculum vitae to sb.icgeb@gmail.com by 20 February 2015</p>
]]></description>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/21538/senior-research-fellow-at-all-india-institute-of-medical-sciences-aiims-delhi-delhi-delhi</guid>
  <pubDate>Wed, 11 Mar 2015 03:06:10 -0500</pubDate>
  <link></link>
  <title><![CDATA[SENIOR RESEARCH FELLOW at All India Institute of Medical Sciences (AIIMS Delhi) - Delhi, Delhi]]></title>
  <description><![CDATA[
<p>Applications are invited from eligible candidates for the following temporary post in an ICMR funded Research Project entitle “An Investigation to find out reasons for Phenotypic Heterogeneity/Variability in 22q11.2 Microdeletion Syndrome” in Department of Reproductive Biology, AIIMS, New Delhi PI: Dr. Ashutosh Halder, Professor, Department of Reproductive Biology </p>

<p>Name of the post: Senior Research Fellow (SRF) <br />Duration: 2 year <br />Salary: Rs. 28000/- per month + 30% HRA <br />Eligibility: MSc (life sciences) with 2 years research experience, NET/GATE qualified <br />Desirable: Experience in the field of Genomics, Epigenomics &amp; Bioinformatics <br />SELECTION PROCEDURE FOR ALL INDIA INSTITUTE OF MEDICAL SCIENCES (AIIMS DELHI) – SENIOR RESEARCH FELLOW POST: </p>

<p>Candidates can apply on or before 15/03/2015 <br />No Detailed information about the selection process is mentioned in the recruitment notification <br />HOW TO APPLY FOR SENIOR RESEARCH FELLOW VACANCY IN ALL INDIA INSTITUTE OF MEDICAL SCIENCES (AIIMS DELHI): </p>

<p>Deadline: 15.03.15 Submit your C.V in Room No. 2099 (Molecular Cytogenetics Lab), 2nd floor, Reproductive Biology, All India Institute of Medical Sciences, New Delhi-110029 or Email CV to: ashutoshhalder@gmail.com Your CV should include the details of your work experience &amp; degrees along with two references with e-mail and contact number Only 10 shortlisted (on merit) candidates will be invited for interview. No TA/DA will be applicable for the same</p>
]]></description>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/20959/research-associate-and-jrf-positions-in-the-structural-and-computational-biology-group-at-icgeb</guid>
  <pubDate>Mon, 02 Feb 2015 23:00:37 -0600</pubDate>
  <link></link>
  <title><![CDATA[Research Associate and JRF positions in the Structural and Computational Biology Group at ICGEB]]></title>
  <description><![CDATA[
<p>Research Associate and JRF positions in the Structural and Computational Biology Group starting 1st March 2015. Collaborative projects include work on:</p>

<p>a) bioinformatics, systems and computational biology <br />b) malaria <br />c) drug discovery <br />d) genomics <br />e) microbiology <br />f) metabolic disorders <br />g) molecular medicine</p>

<p>Eligibility: Applicants must have one of the following :</p>

<p>1) INSPIRE award for undertakig either PhD or Postdoctoral research; <br />2) SPM award for PhD; <br />3) JRF for pursuing PhD from CSIR/DBT/ICMR</p>

<p>Interest and experience in Biochemistry/Bioinformatics/Biophysics/ Chemistry/Genomics/Molecular Biology/ is essential.</p>

<p>Submit curriculum vitae to sb.icgeb@gmail.com by 20 February 2015</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/21064/jrf-project-assistant-recruitment-at-shillong-%E2%80%93-bioinformatics-centre-dic</guid>
  <pubDate>Sat, 07 Feb 2015 06:00:23 -0600</pubDate>
  <link></link>
  <title><![CDATA[JRF / Project Assistant Recruitment at Shillong – Bioinformatics Centre (DIC)]]></title>
  <description><![CDATA[
<p>3 Vacancies at Bioinformatics Centre (DIC) For M.Tech/M.Sc. Degree Candidates. Apply Before 15th February,2015</p>

<p>Bioinformatics Centre (DIC) invites applications for the following posts:</p>

<p>Job Number: 01<br />Job Designation: Junior Research Fellow (JRF)<br />Number of Vacancy: 02 (Two)<br />Educational Qualification:<br />M.Tech/M.Sc. in Life Sciences/Botany/Zoology/Biochemistry/Biotechnology/Bioinformatics.<br />Desirable Qualification:<br />Aptitude for Bioinformatics and Computer Programming/Next generation sequencing data analysis.</p>

<p>Job Number: 02<br />Job Designation: Project Assistant<br />Number of Vacancy: 01 (One)<br />Educational Qualification:<br />Graduation in Science.<br />Desirable Qualification:<br />Experience of working in a Life Science/Plant Biotechnology Lab.</p>

<p>Place of Work: Shillong</p>

<p>How To Apply For Opening:<br />The applications through email bicnehu@gmail.com or post must reach the undersigned within 15 days from the date of publication of this advertisement.</p>

<p>Last Date To Apply: 15th February,2015</p>

<p>Contact Address: Bioinformatics Centre (DIC),Shillong-793022</p>

<p>Advertisement Details: Employment News (31 January – 6 February) Page 28</p>
]]></description>
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