Farhan's blogs: An Optimistic View of a Bioinformatician

 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 ...

GENE EXPRESSION ANALYSIS USING BRB ARRAY TOOL In    this tutorial I've discussed about all the basic requirements to carry out the Gene Expression Analysis using BRB-Array Tool.Watch the videos to make it understandable and helps you fully to use these tools with your data science related research projects. Part 1 Part 2 Basic Requirements for Performing Transcriptomic Analysis using BRB Array Tool As in my previous videos I have talked about the installation of BRB Array Analysis Tool.The next step is to find out the basic things which are required as a input for Big Data Analysis: Raw Data Sample Description File Array Design For instance,if we want to find out that which gene signature is associated with Tumor Recurrence we can use this BRB Array Tool. Thank you Will be waiting for your valuable response.

Installing and Understanding BRB - Array Tool As in our scientific community, its sad that we have very rare opportunities for a  data scientist to carry out his research. Specially in less fortune countries we have very limited resources for data science projects. In this tutorial, I've introduced you guys with one of the tool that will help the biologists and students as well to analyze the Big Data. BRB-ARRAY ANALYSIS TOOLS BRB-ArrayTools is an integrated package for the visualization and statistical analysis of  Microarray gene expression Copy number Methylation   RNA-Seq data Characteristics It was developed by professional statisticians experienced in the analysis of microarray data. The analytic and visualization tools are integrated into Excel as an add-in .  The analytic and visualization tools themselves are developed in the powerful R statistical system, in C and in Java applications.  The system incorporate...