Farhan's blogs: An Optimistic View of a Bioinformatician

The poor quality reads and potential adapter sequences present in your file can be removed using the trimmomatic algorithm. The following video will guide you through the process of how to remove the poor quality reads from your fastq file. #Adapater #Sequences #Linux #Ubuntu

 After generating the Fastq file, first thing you need to check is the quality. The following video will guide you through the process that how to check the quality of fastq files using FASTQC Algorithm. #Fastqc

 How to convert SRA into FASTQ file? Please see the video. #NGS #Sequencing #Datascience

  This is the first part of the lecture series on analyzing sequencing data. The first step is to configure SRA Tool kit on your operating system. #NGS #Sequencing #SRA #Tool #Configuration

 The attached video will explain you the step by step guide to build heatmaps Heatmap using R

 Beast Software BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models.I have briefly explained the installation procedure.         Features of BEAST Software It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology.  BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability.  It includes a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results. Thank you

  An Overview The Hidden Markov Model (HMM) is a relatively simple way to model sequential data. It implies that the Markov Model underlying the data is hidden or unknown to you. More specifically, you only know observational data and not information about the states.  What is a Markov Model? A specific type of model that produces the data but you don’t know what processes are producing it. You basically use your knowledge to make an educated guess about the model’s structure.And that model structure is called Markov Model. As I have tried in my videos to explain HMM in a more simpler way: Part 1 Part 2 HMMs in Sequence Analysis Determine the protein family for the given amino acid sequence. Similar to fitting a speech signal to a word model. Insertions, Deletions and substitutions are allowed. In Computational Biology, a hidden Markov model (HMM) is a statistical approach that is frequently used for modelling biological sequences. HMMs in Speech Recognition Problem Determine ...