Poonam Mahapatra
Bioinformatics Researcher
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NovoGraph: building whole genome graphs from long-read-based de novo assemblies
By Jit 2202 days agogithub.com - NovoGraph: building whole genome graphs from long-read-based de novo assemblies An algorithmically novel approach to construct a genome graph representation of long-read-based de novo sequence assemblies. We then provide a proof of...
Hidden Markov Models, Viterbi Algorithm, Markov Chain Exploration with script
Last updated 4029 days ago by Manisha Mishra Comments (2)Hidden Markov Models, the Viterbi Algorithm, and CpG Islands (in VB6) Problem : The CG island is a stretch of DNA (usually longer than 200 bases) in which the frequency of the CG sequence is higher than other regions. It is also called the CpG...Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies
By Rahul Nayak 2170 days agobitbucket.org - Some parts of a genome may have a very high degree of heterozygosity. This causes contigs for both haplotypes of that part of the genome to be assembled as separate primary contigs, rather than as a contig and an associated haplotig. This can be an...Molecular Bioinformatics Lab (MBL)
The main subject of interest in our laboratory is the study of the relationship among sequence, structure, and function in proteins and nucleic acids. Our research can be divided in two major topics: the study of the sequence-structure...GenomeView: genome browser and annotation editor
By Rahul Nayak 2154 days agosourceforge.net - GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Local and internet files can be loaded.This project has...Scientist Positions @ Gujarat State Biotechnology Mission
Gujarat State Biotechnology Mission invite applications [Online Only] under various projects* namely Gujarat Biodiversity Gene Bank (BioGene), Gujarat Institute of Genomics (GIG), Gujarat Institute of Bioinformatics [GIBS] and Gujarat Institute of...List of tools frequently used while genome assembly
By BioStar 2134 days agoTo decide which strategy should be our “preferred” genome assembly approach based on data rather than my gut-feeling about the “best assembly” I decided to do some testing with a known “true” reference E Coli K12 MG1655The Rogers Lab
The Rogers lab studies evolution of genome structure. We explore the ways that complex mutations like duplications, deletions, rearrangements, and retrogenes can create new genetic material. We study how these new mutations are important for...LAPTI Lab
The main theme of our research is the understanding of how genetic information is decoded from DNA into RNA and proteins. Someone may find this topic a little strange and argue that we already know how this is happening. Translational recoding....ALF--a simulation framework for genome evolution.
By Jit 1860 days agohttp://alfsim.org/#index - Artificial Life Framework (ALF) simulates a root genome into a number of related genomes. Result files include the resulting gene sequences, true tree and true MSAs. A description of ALF can be found in the following article: Daniel A Dalquen,...
