Author: Arafat

  • Creating a Publication Quality Phylogeny Using ggtree

    Creating a Publication Quality Phylogeny Using ggtree

    A decade ago, circa 2012-2013, I used MEGA5 to infer phylogeny using simple Neighbour-Joining methods, and used the figure generated by MEGA5 to present and publish my results. Later, when I started learning other phylogeny reconstruction methods like Maximum Likelihood (ML) and Bayesian (which does not draw the tree for you), I started to explore…

  • How to Find OTUs Using Mothur

    How to Find OTUs Using Mothur

    OTU (Operational Taxonomic Unit) is a convenient way that researchers use to classify a bunch of sequences from different samples into in a taxonomic group based on the similarity. It’s convenient, because one not necessarily need to bother about the actual taxonomic class of the sequence and move forward to analyze the diversity of the…

  • Leveraging Power of Parallelization in UNIX Scripts

    Leveraging Power of Parallelization in UNIX Scripts

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    — 120 reads

    I needed to convert a bunch of bam files back into fastq files. I was implementing a regular for loop to load the files and convert them, one by one, serially. After running the first batch of conversion, I realized that the process is too slow, and is not the best thing to do when…

  • URL Copy Button for non-English Unicode

    URL Copy Button for non-English Unicode

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    If you run a website in non-English language, URLs can be encoded in non-English Unicode character. For example, check the following URL in Bengali: bigganblog.org/2023/12/কীভাবে-গ্রহাণু-শনাক্ত-কর/ This is good for intended audience, since they can just look at the URL and know what is it about in their native language. However, manually copying the URL from…

  • Showing Post View Count in WordPress Block Theme

    Showing Post View Count in WordPress Block Theme

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    In 2023, WordPress released block themes where the single.php code is gone, which is generally used to render single post pages. I have recently experimented with these block themes. You just use the block theme editor within the site, add different blocks by drag-and-drop, and use different patterns, etc. This totally changes the game. I…

  • A tool to visualize fastq alignment with quality-score

    A tool to visualize fastq alignment with quality-score

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    — 153 reads

    Do you need to eyeball through fastq alignment file, with special features to highlight the quality score of each bases? Introducing fastqviz, a Streamlit app which can do just that. I made it quite some time ago to visualize some amplicon data for my own project. You can upload your fastq file. The fastqviz viewer…

  • Argument against “DIY computational drug-discovery” trend in Bangladesh

    I’m seeing a trend that bioscience students from Bangladesh (South Asia in general) are increasingly interested in publishing papers on computational drug design. Many bright students, undergrad or freshly graduated, are actually publishing drug designing related papers in good journals. I have also done similar projects. But now, I think it is a bad trend.…

  • Phylogeny from multi-locus sequences aka MLSA

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    — 130 reads

    For one of my Ph.D. projects, I had to generate phylogeny from multi-locus sequence data. Often I have to repeat similar analyses and need to go back to the previous workflow to check what I actually did. I’m sharing the protocol here mainly to help my future self, and may be this is useful to…

  • What is the alternative to the ‘junk DNA’ hypothesis?

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    — 47 reads

    After completing the human genome sequencing in the 2000s, much of our DNA, even more than half, was considered unnecessary. It was called “junk DNA,” “broken genes” trapped in the genome’s prison, and the DNA fossils of viruses that have been silenced. It was thought these destroyed DNA elements had no purpose and were unrelated…

  • Clad-shift consistency of Dengue in Bangladesh

    Last year I collaborated with cross-institution researchers from Bangladesh led by BCSIR on the severe Dengue outbreak in 2021. The study has been published in the BMC Virology Journal recently. Dengue remains a dangerous endemic disease causing many deaths and suffering in Bangladesh. My contribution was to analyze the phylodynamics of the Dengue virus (DENV).…