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How to create a pangenome of isolated genome sequences using Roary and Prokka?

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Roary is a pangenome genome pipeline, which calculates pangenome of a set of related prokaryotic isolates [1]. It takes annotated assemblies in the gff3 format generated by Prokka [2] and provides the pangenome. The working methodology has been explained in our previous article. In this article, we will learn how to create the pangenome of a few isolated genome sequences using Roary [1] and Prokka [2]. Continue reading “How to create a pangenome of isolated genome sequences using Roary and Prokka?” »

How to do molecular orbital analysis to find d-orbitals involved in bonding in an organometallic compound?

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Structure modeling of chemical compounds finds essential application in the field of cheminformatics. It is used to study the structural stability, metal-ion bonding, the presence of electrons, closed and open shell energies, the reactivity of complexes, molecular orbital analyzes, molecular mechanics, and so on. There is some software available for structural modeling of chemical compounds/complexes and the most widely used are Gaussian [1] and ORCA [2]. Continue reading “How to do molecular orbital analysis to find d-orbitals involved in bonding in an organometallic compound?” »

Bioinformatics and stem cell research- A mini review

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Stem cells are cells that can be differentiated into other types and are thus pluripotent with the ability to become cells of all lineages. Cells found in the blastocyst of embryos are called as embryonic stem cells or ESCs [1, 2] that are considered “gold” standard of pluripotency [3]. There are also adult stem cells found in several tissues for the purpose of repair such as mesenchymal stem cells that have been differentiated into various other tissues [4]. Continue reading “Bioinformatics and stem cell research- A mini review” »

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