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	<title><![CDATA[BOL: BioStar's blogs]]></title>
	<link>https://bioinformaticsonline.com/blog/owner/biostar?offset=10</link>
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	<description><![CDATA[]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44677/exploring-bioinformatics-job-websites-your-gateway-to-a-thriving-career</guid>
	<pubDate>Sat, 19 Oct 2024 13:43:06 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44677/exploring-bioinformatics-job-websites-your-gateway-to-a-thriving-career</link>
	<title><![CDATA[Exploring Bioinformatics Job Websites: Your Gateway to a Thriving Career]]></title>
	<description><![CDATA[<p>Bioinformatics is a rapidly growing field at the intersection of biology, computer science, and data analytics, with applications in healthcare, genomics, drug discovery, and more. As demand increases for skilled professionals who can manage, analyze, and interpret biological data, finding the right job opportunities can be challenging. Fortunately, numerous online platforms cater specifically to bioinformatics professionals, from academia to industry positions.</p><p>Here&rsquo;s a curated list of the top websites offering bioinformatics job opportunities and postdoctoral fellowships worldwide.</p><h3>1. <strong>General Bioinformatics Job Portals</strong></h3><p>These platforms are ideal for bioinformaticians seeking jobs in diverse sectors:</p><ul>
<li>
<p><strong><a href="https://www.nature.com/naturecareers/" target="_new">Nature Careers</a>:</strong> A trusted resource for job seekers in the sciences, Nature Careers offers bioinformatics roles globally. Their specialized search function allows you to filter jobs by keyword, location, and more.</p>
<ul>
<li><a href="https://www.nature.com/naturecareers/searchjobs/?Keywords=bioinformatics" target="_new">Explore Bioinformatics Jobs on Nature Careers</a></li>
</ul>
</li>
<li>
<p><strong><a href="https://jobs.sciencecareers.org/searchjobs/?Keywords=bioinformatics" target="_new">Science Careers</a>:</strong> A job board from the AAAS, this site focuses on STEM jobs, including numerous bioinformatics opportunities in academia and industry.</p>
</li>
<li>
<p><strong><a href="https://euraxess.ec.europa.eu/" target="_new">Euraxess</a>:</strong> Euraxess is the go-to platform for researchers looking for jobs, fellowships, and funding across Europe and beyond. It lists both bioinformatics roles and research grants.</p>
<ul>
<li><a href="https://euraxess.ec.europa.eu/search?keys=bioinformatics" target="_new">Search Bioinformatics Jobs on Euraxess</a></li>
</ul>
</li>
<li>
<p><strong><a href="https://www.researchgate.net/jobs/search/bioinformatics" target="_new">ResearchGate Jobs</a>:</strong> ResearchGate is widely known as a platform for researchers to share publications, but it also has a robust job board featuring bioinformatics positions globally.</p>
</li>
<li>
<p><strong><a href="https://www.findapostdoc.com/?Keywords=bioinformatics" target="_new">FindAPostDoc</a>:</strong> This site is dedicated to helping postdoctoral researchers find positions, with bioinformatics being a popular category.</p>
</li>
<li>
<p><strong><a href="https://academicpositions.com/find-jobs?search=bioinformatics" target="_new">Academic Positions</a>:</strong> Targeting academic roles worldwide, Academic Positions lists bioinformatics jobs at universities and research institutions.</p>
</li>
<li>
<p><strong><a href="https://www.postdocjobs.com/job/search/index?keyword=bioinformatics&amp;location=" target="_new">PostdocJobs.com</a>:</strong> Specializing in postdoctoral roles, this platform is a great resource for early-career researchers looking for bioinformatics-related positions.</p>
</li>
<li>
<p><strong><a href="https://scholarship-positions.com/?s=bioinformatics" target="_new">Scholarship Positions</a>:</strong> In addition to jobs, Scholarship Positions provides information on scholarships, fellowships, and grants related to bioinformatics.</p>
</li>
</ul><h3>2. <strong>Fellowship and Training Opportunities in Bioinformatics</strong></h3><p>For those seeking fellowships or specialized training, these organizations offer postdoctoral programs, grants, and research opportunities:</p><ul>
<li>
<p><strong><a href="https://www.training.nih.gov/research-training/pd/" target="_new">NIH Office of Intramural Training and Education</a>:</strong> The National Institutes of Health offer extensive research training programs for postdocs, including those in bioinformatics.</p>
</li>
<li>
<p><strong><a href="https://new.nsf.gov/funding/opportunities/rui-roa-pui-facilitating-research-predominantly-undergraduate" target="_new">NSF Research Opportunity Awards</a>:</strong> The National Science Foundation funds bioinformatics research at predominantly undergraduate institutions, providing fellowships and grants.</p>
</li>
<li>
<p><strong>Top U.S. Universities:</strong> Many prestigious U.S. institutions, including <a href="https://postdoc.hms.harvard.edu/fellowships" target="_new">Harvard</a>, <a href="https://postdoc.berkeley.edu/" target="_new">Berkeley</a>, <a href="https://postdocs.yale.edu/" target="_new">Yale</a>, <a href="https://postdocs.mit.edu/" target="_new">MIT</a>, <a href="https://postdoc.jhu.edu/" target="_new">Johns Hopkins</a>, <a href="https://postdocs.ucsd.edu/" target="_new">UCSD</a>, and <a href="https://postdocs.cornell.edu/" target="_new">Cornell</a>, offer postdoctoral opportunities in bioinformatics.</p>
</li>
</ul><h3>3. <strong>Country-Specific Job and Fellowship Resources</strong></h3><p>If you're targeting a specific region, these platforms offer bioinformatics opportunities tailored to their respective countries:</p><h4><strong>Canada</strong></h4><ul>
<li><strong><a href="https://capsacpp.ca/" target="_new">CAPS/ACPP</a>:</strong> The Canadian Association of Postdoctoral Scholars provides a job board, including bioinformatics roles in academia.</li>
<li><strong><a href="https://banting.fellowships-bourses.gc.ca/" target="_new">Banting Postdoctoral Fellowships</a>:</strong> A prestigious fellowship program for postdocs in bioinformatics and related fields.</li>
<li><strong><a href="https://www.mitacs.ca/our-programs/elevate-business/" target="_new">Mitacs Elevate</a>:</strong> A Canadian initiative offering fellowships to connect postdoctoral researchers with industry partners.</li>
</ul><h4><strong>United Kingdom</strong></h4><ul>
<li><strong><a href="https://www.ukri.org/" target="_new">UKRI</a>:</strong> The UK Research and Innovation body funds bioinformatics research and offers various grants.</li>
<li><strong><a href="https://royalsociety.org/grants/" target="_new">The Royal Society</a>:</strong> Provides funding schemes for researchers in bioinformatics.</li>
<li><strong><a href="https://marie-sklodowska-curie-actions.ec.europa.eu/" target="_new">Marie Skłodowska-Curie Actions</a>:</strong> The MSCA funds fellowships and doctoral programs across Europe, including bioinformatics-related projects.</li>
<li><strong><a href="https://wellcome.org/grant-funding/schemes" target="_new">Wellcome Trust</a>:</strong> Offers research funding and career development opportunities in health-related fields, including bioinformatics.</li>
</ul><h4><strong>Europe</strong></h4><ul>
<li><strong><a href="https://www.embo.org/funding/fellowships-grants-and-career-support/" target="_new">EMBO Fellowships</a>:</strong> The European Molecular Biology Organization supports bioinformaticians through fellowships and career grants.</li>
<li><strong><a href="https://www.mpg.de/career-programs" target="_new">Max Planck Society</a>:</strong> A leading research organization offering bioinformatics positions and fellowships across Europe.</li>
<li><strong><a href="https://www.helmholtz.de/en/" target="_new">Helmholtz Association</a>:</strong> A major research organization in Germany offering bioinformatics roles in various disciplines.</li>
<li><strong><a href="https://www.leibniz-gemeinschaft.de/en/careers/careers-in-research" target="_new">Leibniz Association</a>:</strong> Offers research opportunities, including bioinformatics, across its numerous institutes.</li>
</ul><h4><strong>Australia and New Zealand</strong></h4><ul>
<li><strong><a href="https://www.arc.gov.au/funding-research/funding-schemes" target="_new">Australian Research Council</a>:</strong> Offers funding and research schemes, including in bioinformatics.</li>
<li><strong>Top Universities:</strong> Universities like <a href="https://www.sydney.edu.au/research.html" target="_new">Sydney</a>, <a href="https://research.unimelb.edu.au/" target="_new">Melbourne</a>, and <a href="https://research.uq.edu.au/" target="_new">Queensland</a> have research programs in bioinformatics.</li>
</ul><h4><strong>Asia</strong></h4><ul>
<li><strong><a href="https://www.jsps.go.jp/english/e-fellow/index.html" target="_new">Japan Society for the Promotion of Science (JSPS)</a>:</strong> Offers fellowships for international researchers in bioinformatics.</li>
<li><strong>Top Institutions:</strong> Universities like <a href="https://www.nus.edu.sg/careers/" target="_new">NUS</a>, <a href="https://english.cas.cn/" target="_new">CAS</a>, and <a href="https://iisc.ac.in/" target="_new">IISc</a> are leading hubs for bioinformatics research.</li>
</ul><h4><strong>Middle East</strong></h4><ul>
<li><strong><a href="https://qrdi.org.qa/en-us/" target="_new">Qatar Research, Development, and Innovation (QRDI)</a>:</strong> Offers research opportunities in bioinformatics.</li>
<li><strong><a href="https://www.kaust.edu.sa/en/" target="_new">KAUST</a>:</strong> A leading university in Saudi Arabia offering bioinformatics research positions.</li>
</ul><h4><strong>Africa</strong></h4><ul>
<li><strong><a href="https://aasciences.africa/" target="_new">African Academy of Sciences</a>:</strong> Provides career opportunities and research funding in bioinformatics across Africa.</li>
</ul><h3>Conclusion</h3><p>The field of bioinformatics is full of exciting opportunities for those with the right skills. Whether you are looking for a postdoc position, research funding, or a long-term job in industry, these platforms are an excellent starting point. Explore, apply, and take the next step in your bioinformatics career!</p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44633/learn-python-with-example</guid>
	<pubDate>Tue, 06 Aug 2024 23:51:51 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44633/learn-python-with-example</link>
	<title><![CDATA[Learn python with example]]></title>
	<description><![CDATA[<div><div><div><p>There are over 21 unique&nbsp;Python project&nbsp;walkthroughs in this content that range from beginner to advanced. See below for the timestamps for these projects:</p><p><span>00:00:00 | How To Navigate These Projects</span><br /><span>---</span><br /><span>00:01:46 | #1 - Quiz Game (Easy)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F5-Python-Projects-For-Beginners%2Fblob%2Fmain%2Fquiz_game.py" target="_blank">https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/quiz_game.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>00:22:00 | #2 - Number Guessing Game (Easy)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F5-Python-Projects-For-Beginners%2Fblob%2Fmain%2Fnumber_guesser.py" target="_blank">https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/number_guesser.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>00:39:49 | #3 - Rock, Paper, Scissors (Easy)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F5-Python-Projects-For-Beginners%2Fblob%2Fmain%2Frock_paper_scissors.py" target="_blank">https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/rock_paper_scissors.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>00:54:40 | #4 - Choose Your Own Adventure Game (Easy)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F5-Python-Projects-For-Beginners%2Fblob%2Fmain%2Fchoose_your_own_adventure.py" target="_blank">https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/choose_your_own_adventure.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>01:06:47 | #5 - Password Manager (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F5-Python-Projects-For-Beginners%2F" target="_blank">https://github.com/techwithtim/5-Python-Projects-For-Beginners/</a><span>&nbsp;</span><br /><span>Fernet Cryptography Documentation:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fcryptography.io%2Fen%2Flatest%2Ffernet%2F" target="_blank">https://cryptography.io/en/latest/fernet/</a><span>&nbsp;</span><br /><span>---</span><br /><span>01:37:37 | #6 - PIG (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects%2Fblob%2Fmain%2Fproject1.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects/blob/main/project1.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>01:59:07 | #7 - Madlibs Generator (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects%2Fblob%2Fmain%2Fproject2.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects/blob/main/project2.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>02:15:04 | #8 - Timed Math Challenge (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects%2Fblob%2Fmain%2Fproject3.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects/blob/main/project3.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>02:28:02 | #9 - Slot Machine (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FPython-Slot-Machine" target="_blank">https://github.com/techwithtim/Python-Slot-Machine</a><span>&nbsp;</span><br /><span>---</span><br /><span>03:20:43 | #10 - Turtle Racing (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FTurtle-Racing-V2" target="_blank">https://github.com/techwithtim/Turtle-Racing-V2</a><span>&nbsp;</span><br /><span>Turtle Docs:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fdocs.python.org%2F3%2Flibrary%2Fturtle.html" target="_blank">https://docs.python.org/3/library/turtle.html</a><span>&nbsp;</span><br /><span>---</span><br /><span>04:13:09 | #11 - WPM Typing Test (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FWPM_Typing_Test" target="_blank">https://github.com/techwithtim/WPM_Typing_Test</a><span>&nbsp;</span><br /><span>Curses Docs:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fdocs.python.org%2F3%2Fhowto%2Fcurses.html" target="_blank">https://docs.python.org/3/howto/curses.html</a><span>&nbsp;</span><br /><span>05:09:43 | #12 - Alarm Clock (Easy)</span><br /><span>Python Project Idea Blog:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fhackr.io%2Fblog%2Fpython-projects" target="_blank">https://hackr.io/blog/python-projects</a><span>&nbsp;</span><br /><span>Sound Effects:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fwww.fesliyanstudios.com%2Froyalty-free-sound-effects-download%2Falarm-203" target="_blank">https://www.fesliyanstudios.com/royalty-free-sound-effects-download/alarm-203</a><span>&nbsp;</span><br /><span>---</span><br /><span>05:22:07 | #13 - Password Generator (Easy)</span><br /><span>Python Project Idea Blog:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fhackr.io%2Fblog%2Fpython-projects" target="_blank">https://hackr.io/blog/python-projects</a><span>&nbsp;</span><br /><span>---</span><br /><span>05:39:16 | #14 - Shortest Path Finder (Advanced)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects-For-Intermediates%2Fblob%2Fmain%2Fpath-finder.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects-For-Intermediates/blob/main/path-finder.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>06:14:53 | #15 - NBA Stats &amp; Current Scores (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects-For-Intermediates%2Fblob%2Fmain%2Fnba-scores.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects-For-Intermediates/blob/main/nba-scores.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>06:38:22 | #16 - Currency Converter (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects-For-Intermediates%2Fblob%2Fmain%2Fcurrency-converter.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects-For-Intermediates/blob/main/currency-converter.py</a><span>&nbsp;</span><br /><span>API: https://free.currencyconverterapi.com/</span><br /><span>---</span><br /><span>06:58:51 | #17 - YouTube Video Downloader (Medium)</span><br /><span>Code: &nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FPython-Beginner-Automation-Projects%2Fblob%2Fmain%2Fyoutube.py" target="_blank">https://github.com/techwithtim/Python-Beginner-Automation-Projects/blob/main/youtube.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>07:09:50 | #18 - Automated File Backup (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FPython-Beginner-Automation-Projects%2Fblob%2Fmain%2Fbackup.py" target="_blank">https://github.com/techwithtim/Python-Beginner-Automation-Projects/blob/main/backup.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>07:21:18 | #19 - Mastermind/4 Color Match (Advanced)</span><br /><span>---</span><br /><span>07:48:20 | #20 - Aim Trainer (Advanced)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FPython-Aim-Trainer" target="_blank">https://github.com/techwithtim/Python-Aim-Trainer</a><span>&nbsp;</span><br /><span>---</span><br /><span>08:39:20 | #21 - Advanced Python Scripting (Advanced)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FPython-Scripting-Project" target="_blank">https://github.com/techwithtim/Python-Scripting-Project</a><span>&nbsp;</span></p></div></div></div>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44616/basics-of-blast-programs</guid>
	<pubDate>Fri, 26 Jul 2024 06:04:26 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44616/basics-of-blast-programs</link>
	<title><![CDATA[Basics of BLAST Programs !]]></title>
	<description><![CDATA[<p>The Basic Local Alignment Search Tool (BLAST) is a powerful bioinformatics program used to compare an input sequence (such as DNA, RNA, or protein sequences) against a database of sequences to find regions of similarity. Developed by the National Center for Biotechnology Information (NCBI), BLAST is widely used for identifying species, finding functional and evolutionary relationships between sequences, and predicting the function of novel sequences.</p><p>Key Features of BLAST:<br />1. Sequence Comparison: BLAST searches for local alignments between the query sequence and sequences in a database. It identifies regions of similarity, which can help infer functional and evolutionary relationships.</p><p>2. Speed and Efficiency: BLAST uses heuristic algorithms, making it faster than exhaustive search methods, suitable for large-scale database searches.</p><p>3. Versatility: There are several versions of BLAST for different types of sequence comparisons:<br /> - blastn: Compares a nucleotide query sequence against a nucleotide sequence database.<br /> - blastp: Compares a protein query sequence against a protein sequence database.<br /> - blastx: Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> - tblastn: Compares a protein query sequence against a nucleotide sequence database translated in all reading frames.<br /> - tblastx: Compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.</p><p>4. Scoring and E-value: BLAST results are scored based on the quality and length of the alignments. The E-value (expect value) indicates the number of alignments one can expect to find by chance, with lower E-values representing more significant matches.</p><p>5. Output Formats: BLAST provides results in various formats, including plain text, HTML, XML, and JSON, making it adaptable for different types of analyses and integrations with other tools.</p><p>Applications of BLAST:<br />- Genomic Research: Identifying genes, understanding genetic diversity, and mapping genome sequences.<br />- Protein Function Prediction: Inferring the function of unknown proteins by comparing them to known protein sequences.<br />- Evolutionary Studies: Exploring evolutionary relationships between organisms by comparing their genetic material.<br />- Medical Research: Identifying pathogens, understanding disease mechanisms, and developing treatments by comparing sequences of interest.</p><p>Overall, BLAST is an essential tool in bioinformatics, offering a reliable and efficient way to analyze and interpret biological sequence data.</p>]]></description>
	<dc:creator>BioStar</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44614/online-resources-on-must-read-papers-in-evolutionary-biology</guid>
	<pubDate>Fri, 26 Jul 2024 01:39:14 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44614/online-resources-on-must-read-papers-in-evolutionary-biology</link>
	<title><![CDATA[Online resources on must-read papers in evolutionary biology]]></title>
	<description><![CDATA[<pre>Online resources on must-read papers in evolutionary biology, for a literature club.<br /><br />Below is a summary of all answers that we received.

All the best,

Jana and Xiaoyan

1.       *Nick Barton:*

- The textbook "Evolution" by Nick Barton, with resources for
  exploring the literature: Barton, N. H., Briggs, D. E. G., Eisen, J.
  A., Goldstein, D. B., &amp; Patel, N. H. (2007). Evolution. Cold Spring
  Harbor Laboratory Press.

- Papers from a course named "Classics in Evolutionary Biology":

Evolutionary Synthesis
1. Haldane, J. B. S. 1932. The causes of evolution. Longmans. New York.
   (esp. Ch. IV).
2. Fisher, R. A. 1930. The genetical theory of natural selection. Oxford
   University Press, Oxford. Selected Sections - Fundamental Theorem.

Genetic Variation
1a. Lewontin, R. C., and J. L. Hubby. 1966. A molecular approach to
the study of genic heterozygosity in natural populations. II. Amount
of variation and degree of heterozygosity in natural populations of
Drosophila pseudoobscura. Genetics. 54:595-609.

1b. Sachidandam et al. 2001. A map of human genome sequence variation
containing 1.42 million single nucleotide polymorphisms. 409: 928-33.

2. Wright S., Dobzhansky T., Hovanitz W. 1942 Genetics of natural
populations VII The allelism of lethals in the third chromosome of
Drosophila pseudoobscura. Genetics 27: 363-394.

Recombination and evolution
1. Hill, W. G., and A. Robertson. 1966. The effect of linkage on limits
to artificial selection. Genet. Res. 8:269-294.

2. Maynard Smith and Haigh. 1974. The hitch-hiking effect of a favourable
gene. Genet. Res. 23: 23-35.

Understanding sequence variation
1. Begun D. J., Aquadro C. F., 1992 Levels of naturally occurring DNA
polymorphism correlate with recombination rate in Drosophila melanogaster.
Nature 356: 519-520.

2. Green R. E., Reich D., P&auml;&auml;bo S., 2010 A draft sequence of the
Neandertal genome. Science 328: 710-722.

Quantitative Genetics:  variation in complex traits
1. Galton F., 1877 Typical laws of heredity. Nature 15: 492-495-
512-514- 532-533.

2. Turelli M., 1984 Heritable genetic variation via
mutation-selection balance: Lerch's Zeta meets the abdominal
bristle. Theor. Popul. Biol. 25: 138-193.

Quantitative Genetics:  finding the genes
1. Shrimpton A. E., Robertson A., 1988 The Isolation of polygenic factors
controlling bristle score in Drosophila melanogaster II Distribution of
third chromosome bristle effects within chromosome sections. Genetics
118: 445-459.

2. Boyle E. A., Li Y. I., Pritchard J. K., 2017 An expanded view of
complex traits: from polygenic to omnigenic. Cell 169: 1177-1186.

Neutral Evolution
1. Kimura, M. 1968. Evolutionary rate at the molecular level. Science.
217:624-626.

2a. Kern A. D., Hahn M. W., 2018 The Neutral Theory in Light of Natural
Selection. Molecular Biology and Evolution 110: 21077-6.

2b. Jensen J. D., Payseur B. A., Stephan W., Aquadro C. F., Lynch M.,
Charlesworth D., Charlesworth B., 2018 The importance of the Neutral Theory
in 1968 and 50 years on: a response to Kern and Hahn 2018. Evolution 112:
2109-4.

2c. Ellegren &amp; Galtier. 2016. Determinants of genetic diversity. Nature
Reviews Genetics.

Mutation and Genetic Variability
1. Luria, S. E., and M. Delbr&uuml;ck. 1943. Mutations of Bacteria from Virus
Sensitivity to Virus Resistance. Genetics. 28(6):491-511.

2. Hill, W G. 1982. "Rates of Change in Quantitative Traits From Fixation
of New Mutations." Proceedings of the National Academy of Sciences (U.S.A.)
79: 142-45.

Testing for selection
1. McDonald &amp; Kreitman. 1991. Adaptive protein evolution at the Adh locus
in Drosophila. Nature.

2. Begun, et al. Mol. Biol. Evol. 16, 1816-1819 (1999).

3. Siddiq et al. 2016. Experimental test and refutation of a classic case
of molecular adaptation in Drosophila melanogaster.  Nature Ecology &amp;
Evolution.

The shifting balance
1. Wright, S. 1932. The roles of mutation, inbreeding, crossbreeding and
selection in evolution. Proceedings of the VI International Congress of
Genetics: 1. pp 356-366.

2. Coyne, J.A., N.H. Barton, and M. Turelli. 1997. A critique of Wright's
shifting balance theory of evolution.  Evolution 51: 643-671.

3. Barton. 2016. Sewall Wright on Evolution in Mendelian Populations and
the "Shifting Balance". Genetics.

Evolution of Sex
1.  Muller, H.J. 1964. The relation of recombination to mutational advance.
Mutation Res. 1(1):2-9

2. McDonald et al. 2016. Sex speeds adaptation by altering the dynamics of
molecular evolution. Nature.

Kin Selection, Cooperation, and Conflict
1. Hamilton, W. D. 1964. The genetical evolution of social behaviour I.
Journal of Theoretical Biology. 7:1-52.

2. Trivers, R. L. 1974 Parent-offspring conflict. American Zoologist.
14(1):249-264.

Sexual Selection
1. Zahavi, A. 1975. Mate selection - a selection of a handicap. J. Theor.
Biol. 53:205-214.

2. Kirkpatrick, M., and Ryan, M.J. 1991. The evolution of mating
preferences and the paradox of the lek. Nature. 350:33-38.

Fitness Landscapes
1. Dean, A. 1995. A Molecular Investigation of Genotype by Environment
Interactions. Genetics. 139:19-33.

2. Costanzo et al. 2010. The Genetic Landscape of a Cell. Science.

Speciation
1. Coyne, J. A., and H. A. Orr. 1989. Patterns of speciation in Drosophila.
Evolution. 43:362-381.

2. Corbett-Detig et al. 2013. Genetic incompatibilities are widespread
within species. Nature.

2.       *Marcos Antezana:*

Valen, L. v. 1975. Energy and Evolution. University of Chicago, Department
of Biology.

3.       *Remco Folkertsma:*

1. The work by Hopi Hoekstra on local adaptation and oldfield mice

2. Poelstra, J. W., Vijay, N., Bossu, C. M., Lantz, H., Ryll, B., M&uuml;ller,
I., ... &amp; Wolf, J. B. (2014). The genomic landscape underlying phenotypic
integrity in the face of gene flow in crows. Science, 344(6190), 1410-1414.

4.       *Joshka Kaufmann and Leslie Turner*

They offer us a link to 'papers every evolutionary biologist should read',
the papers are collected by Leslie Turner.
https://static1.squarespace.com/static/53e8cb7ce4b02c4bc3aeeee4/t/5ab8fcb670a6ad55c67fcdf4/1522072758665/EvoBioClassicsRefList.pdf

5.       *Sarah Stockwell*

Matt Ridley collected classic papers in evolutionary biology and printed
part of these papers in his book Evolution (see Matt Ridley. Evolution
(Univ. of Oxford Press, 2nd edition, 2004))
</pre>]]></description>
	<dc:creator>BioStar</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44506/mosquito-species-known-for-transmitting-the-dengue-virus</guid>
	<pubDate>Wed, 03 Apr 2024 00:05:51 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44506/mosquito-species-known-for-transmitting-the-dengue-virus</link>
	<title><![CDATA[Mosquito species known for transmitting the Dengue virus]]></title>
	<description><![CDATA[<p><span>Here is a list of mosquito species known for transmitting the Dengue virus along with essential and applied information about each species:</span><br /><br /><span>1. Aedes aegypti:</span><br /><span>- Geographical Distribution: Found in tropical and subtropical regions worldwide.</span><br /><span>- Biting Behavior: Daytime biter, prefers feeding indoors, often around human dwellings.</span><br /><span>- Role in Dengue Transmission: Primary vector responsible for transmitting Dengue virus to humans.</span><br /><br /><span>2. Aedes albopictus (Asian tiger mosquito):</span><br /><span>- Geographical Distribution: Found in tropical, subtropical, and temperate regions worldwide.</span><br /><span>- Biting Behavior: Daytime biter, feeds both indoors and outdoors, aggressive feeder.</span><br /><span>- Role in Dengue Transmission: Secondary vector, can transmit Dengue virus to humans.</span><br /><br /><span>3. Aedes polynesiensis:</span><br /><span>- Geographical Distribution: Found in Pacific Islands and coastal regions.</span><br /><span>- Biting Behavior: Daytime biter, prefers feeding outdoors, often near coastal areas.</span><br /><span>- Role in Dengue Transmission: Vector of Dengue virus in specific geographic regions.</span><br /><br /><span>4. Aedes scutellaris:</span><br /><span>- Geographical Distribution: Found in Southeast Asia, Pacific Islands, and coastal regions.</span><br /><span>- Biting Behavior: Daytime feeder, active in shaded areas, prefers outdoor environments.</span><br /><span>- Role in Dengue Transmission: Vector of Dengue virus, particularly in coastal areas.</span><br /><br /><span>5. Aedes africanus:</span><br /><span>- Geographical Distribution: Found in parts of Africa, including forested areas.</span><br /><span>- Biting Behavior: Daytime feeder, prefers shaded areas, bites humans and other animals.</span><br /><span>- Role in Dengue Transmission: Vector of Dengue virus in African regions.</span><br /><br /><span>Understanding the geographical distribution and biting behavior of these mosquito species is crucial for implementing effective control and prevention strategies to reduce Dengue virus transmission.</span></p>]]></description>
	<dc:creator>BioStar</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44401/bioinformatics-tools-for-phylogeny</guid>
	<pubDate>Mon, 06 Nov 2023 03:09:59 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44401/bioinformatics-tools-for-phylogeny</link>
	<title><![CDATA[Bioinformatics Tools for Phylogeny !]]></title>
	<description><![CDATA[<p><span>Direct access to the individual tools available on this server.</span></p><table summary="list of individual tools">
<thead>
<tr><th>Multiple Alignment:</th><th>Phylogeny:</th><th>Tree viewers:</th><th>Utilities:</th></tr>
</thead>
<tbody>
<tr>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=muscle">MUSCLE</a></td>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=phyml">PhyML</a></td>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=treedyn">TreeDyn</a></td>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=gblocks">Gblocks</a></td>
</tr>
<tr>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=tcoffee">T-Coffee</a>&nbsp;/&nbsp;<a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=expresso">3DCoffee</a></td>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=tnt">TNT</a></td>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=drawgram">Drawgram</a></td>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=jalview">Jalview</a></td>
</tr>
<tr>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=clustalw">ClustalW</a></td>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=bionj">BioNJ</a></td>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=drawtree">Drawtree</a></td>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=readseq">Readseq</a></td>
</tr>
<tr>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=probcons">ProbCons</a></td>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=mrbayes">MrBayes</a></td>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=atv">ATV (A Tree Viewer)</a></td>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/data_converter.cgi">Built-in converter</a></td>
</tr>
</tbody>
</table>]]></description>
	<dc:creator>BioStar</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44379/understanding-and-confronting-amr-the-looming-threat-of-antimicrobial-resistance</guid>
	<pubDate>Wed, 06 Sep 2023 00:45:31 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44379/understanding-and-confronting-amr-the-looming-threat-of-antimicrobial-resistance</link>
	<title><![CDATA[Understanding and Confronting AMR: The Looming Threat of Antimicrobial Resistance]]></title>
	<description><![CDATA[<p>Antimicrobial resistance (AMR) is a complex and pressing challenge in the field of microbiology and public health. It occurs when microorganisms, such as bacteria, viruses, and fungi, develop mechanisms to withstand the effects of antimicrobial agents, including antibiotics, antivirals, and antifungals, rendering these drugs ineffective in treating infections. The emergence and spread of AMR are primarily driven by the overuse and misuse of these drugs in human medicine, agriculture, and livestock production. This selective pressure encourages the survival and proliferation of resistant strains, threatening our ability to combat infectious diseases effectively.</p><p>The consequences of AMR are profound and multifaceted. Medically, it leads to treatment failures, prolonged illnesses, and increased mortality rates, as common infections become more challenging to manage. The economic burden of AMR is substantial, as it escalates healthcare costs due to longer hospital stays, the need for more potent and expensive drugs, and the potential loss of productivity in affected individuals. Furthermore, AMR jeopardizes global health security, as the emergence of multidrug-resistant pathogens makes it increasingly difficult to respond to infectious disease outbreaks and bioterrorism threats.</p><p>To address AMR, a multidisciplinary approach is essential. This includes improved antimicrobial stewardship practices in healthcare settings, raising public awareness about the responsible use of antibiotics, and developing rapid diagnostic tests to guide precise treatment decisions. Additionally, there is a crucial need for continued research into the development of novel antimicrobial agents and vaccines. Collaborative efforts among scientists, clinicians, policymakers, and the pharmaceutical industry are essential to mitigate the impact of AMR and ensure that our arsenal of effective treatments remains robust in the face of evolving microbial threats. In the absence of concerted global action, the specter of untreatable infections looms, underscoring the urgency of addressing AMR as a critical public health priority.</p>]]></description>
	<dc:creator>BioStar</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44267/free-books-on-machine-learning-and-artificial-intelligent</guid>
	<pubDate>Thu, 16 Mar 2023 00:10:24 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44267/free-books-on-machine-learning-and-artificial-intelligent</link>
	<title><![CDATA[Free Books on Machine Learning and Artificial Intelligent !]]></title>
	<description><![CDATA[<div><p>An Introduction to Statistical Learning<br />This book provides a broad and less technical treatment of key topics in statistical learning. Each chapter includes an R lab. This book is appropriate for anyone who wishes to use contemporary tools for data analysis.</p><p>https://hastie.su.domains/ISLR2/ISLRv2_website.pdf</p><p>Python Data Science Handbook<br />You&rsquo;ll learn how to use the core libraries essential for working with data in Python: particularly IPython, NumPy, Pandas, Matplotlib, Scikit-Learn, and related packages. This resource is perfect for tackling day-to-day issues such as cleaning, manipulating, and transforming data &mdash; or building machine learning models.</p><p>https://jakevdp.github.io/PythonDataScienceHandbook/</p><p>Dive into Deep Learning<br />Interactive deep learning book with code, math, and discussions. Implemented with PyTorch, NumPy/MXNet, JAX, and TensorFlow. Adopted at 400 universities from 60 countries</p><p>https://d2l.ai/</p><p>Approaching (Almost) Any Machine Learning Problem<br />This book is for people who have some theoretical knowledge of machine learning and deep learning and want to dive into applied machine learning. The book is more oriented towards how and what should you use to solve machine learning and deep learning problems. The book is for you if you are looking for guidance on approaching machine learning problems.</p><p>https://github.com/abhishekkrthakur/approachingalmost/blob/master/AAAMLP.pdf</p></div>]]></description>
	<dc:creator>BioStar</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44257/calculate-the-significance-of-the-difference-between-two-trends</guid>
	<pubDate>Tue, 14 Mar 2023 05:41:53 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44257/calculate-the-significance-of-the-difference-between-two-trends</link>
	<title><![CDATA[Calculate the significance of the difference between two trends]]></title>
	<description><![CDATA[<div><div><div><div><div><div><div><div><div><div><p>To calculate the significance of the difference between two trends, you can use a statistical test such as a t-test or ANOVA (analysis of variance). Here are the general steps to follow:</p><ol>
<li>
<p>Define your null hypothesis (H0) and alternative hypothesis (H1). For example, H0 might be that there is no significant difference between the two trends, while H1 might be that there is a significant difference.</p>
</li>
<li>
<p>Collect data on the two trends. Make sure that the data is independent, normally distributed, and has equal variances.</p>
</li>
<li>
<p>Calculate the means and standard deviations of each trend.</p>
</li>
<li>
<p>Calculate the test statistic using a t-test or ANOVA. The test statistic will depend on the specific test you choose, but it will generally compare the difference in means between the two trends to the variability within each trend.</p>
</li>
<li>
<p>Determine the p-value associated with the test statistic. The p-value represents the probability of obtaining a test statistic as extreme as the one you calculated, assuming that the null hypothesis is true.</p>
</li>
<li>
<p>Compare the p-value to your chosen significance level (usually 0.05 or 0.01). If the p-value is less than or equal to the significance level, reject the null hypothesis and conclude that there is a significant difference between the two trends. If the p-value is greater than the significance level, fail to reject the null hypothesis and conclude that there is not enough evidence to support a significant difference.</p>
</li>
</ol><p>It's important to note that the specific details of each step will depend on the type of test you choose and the software you use to perform the analysis.</p><p>The most common methods for comparing means include:</p><table>
<thead>
<tr><th>Methods</th><th>R function</th><th>Description</th></tr>
</thead>
<tbody>
<tr>
<td>T-test</td>
<td>t.test()</td>
<td>Compare two groups (parametric)</td>
</tr>
<tr>
<td>Wilcoxon test</td>
<td>wilcox.test()</td>
<td>Compare two groups (non-parametric)</td>
</tr>
<tr>
<td>ANOVA</td>
<td>aov() or anova()</td>
<td>Compare multiple groups (parametric)</td>
</tr>
<tr>
<td>Kruskal-Wallis</td>
<td>kruskal.test()</td>
<td>Compare multiple groups (non-parametric)<br /><br /></td>
</tr>
</tbody>
</table></div></div></div></div></div></div></div></div></div></div>]]></description>
	<dc:creator>BioStar</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44234/steps-to-find-palindrome-in-genomes</guid>
	<pubDate>Thu, 09 Mar 2023 02:56:54 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44234/steps-to-find-palindrome-in-genomes</link>
	<title><![CDATA[Steps to find palindrome in genomes !]]></title>
	<description><![CDATA[<div><div><div><div><div><div><div><div><div><div><p>Palindromes are sequences of nucleotides that read the same backward as forward. They can be present in genomes and have various biological functions. Here are some methods for discovering palindromes in genomes:</p><ol>
<li>
<p>Direct sequence search: One of the simplest ways to discover palindromes is to search the genome sequence directly for palindromic sequences using pattern matching tools, such as regular expressions or string algorithms. This approach can be useful for discovering simple palindromes, but may miss more complex palindromic structures.</p>
</li>
<li>
<p>Dot plot analysis: Dot plot analysis is a graphical method that can be used to identify palindromic regions in a genome. It involves plotting the genome sequence against itself and examining the diagonal patterns that emerge. Palindromic regions will appear as symmetrical patterns along the diagonal.</p>
</li>
<li>
<p>Restriction enzyme analysis: Some restriction enzymes, such as EcoRI and HindIII, recognize palindromic sequences and cleave DNA at these sites. By digesting the genome with these enzymes and examining the resulting fragments, palindromic regions can be identified.</p>
</li>
<li>
<p>Next-generation sequencing: High-throughput sequencing technologies, such as PacBio and Oxford Nanopore, can generate long reads that can span entire palindromic regions. By mapping these reads to the genome, palindromic regions can be identified and characterized.</p>
</li>
<li>
<p>Comparative genomics: Comparing the genomes of related species can also reveal palindromic regions that are conserved across evolutionarily divergent lineages. This approach can help identify functional palindromes that are under selective pressure.</p>
</li>
</ol><p>Overall, the discovery of palindromic sequences in genomes can be accomplished using a variety of methods, each with their own advantages and limitations. A combination of these methods can provide a comprehensive understanding of the palindromic landscape of a genome.</p></div></div></div></div></div></div></div></div></div></div>]]></description>
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