Farhan's blogs: An Optimistic View of a Bioinformatician

SIMPLE METHODS TO CREATE GANTT CHARTS USING MS EXCEL In this video I've explained two of the most simplest methods for creating the gantt charts.These charts helps the biological researchers for planning and scheduling their projects.They are helpful to assess how much time your project will take to achieve the end results. What is a Gantt Chart? A Gantt chart is a horizontal bar chart developed as a production control tool in 1917 by Henry L. Gantt , an American engineer and social scientist.This chart provides a graphical illustration of a schedule that helps to plan, coordinate, and track specific tasks in a project. On the left of the chart is the list of the activities and along the top a suitable time scale.Each activity is represented by a bar and length of the bar represents the start date,duration and end of the activity. A Useful Information that we can get from Gantt Charts v What the various      activities are? v When the act...

A TUTORIAL FOR THE BEGINNERS:BLAST AND ENSEMBL GENE BROWSER In these videos I have explained about how to extract the gene sequence and find out the orthologs using BLAST in ENSEMBL GENOME BROWSER. BLAST(BASIC LOCAL ALLIGNMENT SEARCH TOOL) The program compares nucleotide or protein sequences to sequencedatabases and calculates the statistical significance. (BLAST) finds regions of local similarity between sequences. FOR MORE DETAILS WATCH THE VIDEOS THANK YOU

A Tutorial to View the Whole Genome Synteny using Biomart in ENSEMBL In this video I have explained few steps to view the Whole Genome Synteny. WHAT IS A SYNTENY? The co-localization of genetic loci on the same chromosome within an individual or species. EXAMPLE GENE SYNTENY MAP TBX5 Synteny map depicts the presence of 6 genes in the upstream (1mb) region and only one gene in the downstream (1mb) region. COMPARATIVE SYNTENY MAP THANK YOU Waiting for your Valuable Feedback

A Tutorial on How to View Synteny Using Ensembl Genome Browser HOW A SYNTENY ANALYSIS HELPS A BIOLOGIST? Synteny provides a framework in which conservation of homologous genes and gene order is identified between genomes of different species. Synteny analysis is regularly performed on assembled sequences that are fragmented, neglecting the fact that most methods were developed using complete genomes. THANK YOU WAITING FOR YOUR VALUABLE RESPONSE

A TUTORIAL ON HOW TO USE BIOMART IN ENSEMBL BIOMART : In this video I have explained the usage of BIOMART. It is a simplest online tool that permits extraction of information with no programming information or comprehension of the basic database structure. HOW TO USE A BIOMART: 1. Selection of Database Type  Following are the databases that can be chosen : Ensembl gene Ensembl variation Ensembl regulation  Vega 2. Selection of Database Species Data available for all the Species including Ensembl genes,Ensembl variation, Ensembl regulation and Vega. 3. Filtration of Input Data BioMart permits you to confine your question with data that you know, e.g: input a list of IDs, restrict to a region. You can access the filter page by clicking on the "Filters" button located on the left panel. 4.Selection of Attributes This option permits you to choose your ideal yield; the default yield is  Ensembl...

ENSEMBL GENOME BROWSER ENSEMBL provides a genome browser that acts as a single point of access to annotated genomes for mainly vertebrate species. As in this tutorial I have explained some of the basic features of ENSEMBL. Please watch the video Ensembl contains information on chordate genomes, including human, mouse, rat, zebrafish, panda, and takifugu. BASIC FEATURES OF ENSEMBL: Information such as gene sequence, splice variants and further annotation can be retrieved at the genome, gene and protein level. This includes information on protein domains, genetic variation, homology, syntenic regions and regulatory elements. Coupled with analyses such as whole genome alignments and effects of sequence variation on protein, this powerful tool aims to describe a gene or genomic region in detail.

A Tutorial for Generating a Phylogenetic Tree:Simplest and Comprehensive guide As I have explained earlier in my last video,how to install a MEGA Software.Now moving to the next step that is generating a phylogenetic tree.So In this video,I am talking about how to generate a tree using this Software. Step wise Representation for generating a Phylogenetic Tree Acquiring the Sequences MEGA5 opens its own browser window to show a BLAST page from National Center for Biotechnology Information (NCBI) from where it gets the sequences . Alligning the Sequence The next step is allignment of the sequences that we have downloaded from NCBI in FASTA format. Two methods can be used for Multiple Sequence Allignment :  Muscle CLUSTAL W   Estimating a PhylogeneticTree There are several widely used methods for estimating phylogenetic trees Neighbor Joining  UPGMA  Bayesian Inference  Maximum Likelihoo...

Phylogenetic Analysis:A tutorial for  how to  Install MEGA Software In this video,I have explained about the installation of MEGA Software step wise. MEGA SOFTWARE MEGA is a useful software in constructing phylogenies and visualizing them, and also for data conversion. Features  It can easily convert Alignment files to PHYLIP. The MEGA tree explorer is helpful in editing trees very easily, subtrees can also be selected and edited separately. The input formats are NEWICK, PHYLIP, MEGA, and NEXUS. The Phylogenetic tree can also be converted in newick format.

BASICS OF PHYLOGENETICS: Learn how  to Calculate Evolutionary Distances Phylogenetic Tree Analysis Calculations for constructing a Phylogenetic tree? The calculations for construction of phylogenetic trees can be handled in two ways: By Distance Matrix data By Discrete character data Distance Based Matrix The distance Matrix data based on evolutionary distances.For constructing a phylogenetic tree,in a distance based method each nucleotide changes equally. Evolutionary Distance Evolutionary distance refers to the number of nucleotide substitutions per site between two homologous DNA sequences or the number of amino acid substitutions per site between two homologous protein sequences. For more details watch the following video THANK YOU

BASICS OF PHYLOGENETICS : Computational  Analysis of Distance and Character based methods Distance based Method : Transform the sequence data into pairwise distances and then use the matrix during tree building ignoring the characters. The distance based phylogenetic methods measure the distance from the dissimilarity observe between pairs of sequences, computed on the basis of sequence alignment.  The main assumption of distance based methods is homologous and that tree branches can sum-up. Character based Method: It use the alligned sequences directly during tree inference. For more details please watch the video below THANK YOU WAITING FOR YOUR FEEDBACK

BASIC GUIDELINE TO UNDERSTAND ROOTED AND UNROOTED TREES IN PHYLOGENETICS   What is a  PHYLOGENETIC TREE? Phylogenetic trees represent hypothesis about the evolutionary relationships among a group of organisms. A phylogenetic tree may be built using morphological (body shape), biochemical, behavioral, or molecular features of species or other groups.In building a tree, we organize species into nested groups based on shared derived traits (traits different from those of the group's ancestor). HOW TO DRAW A PHYLOGENETIC TREE? In a phylogenetic tree, the species of interest are shown at the tips of the tree's branches. The branches themselves connect up in a way that represents the evolutionary history of the species that is, how we think they evolved from a common ancestor through a series of divergence (splitting-in-two) events.For more details watch the video below: THANK YOU

The Most Basic guide to learn Phylogenetics Introduction v   The term Phylogenetics is derived from Greek word where Phylo meaning tribe or clan Genetikos meaning genesis, origin or birth. v   It is mostly used to study the evolutionary history of species or gene sequences.  Currently, It is perhaps the most widely used bioinformatics application. v   See the following example before we go into further details of Phyloegenetics. WATCH THE VIDEO BELOW FOR MORE DETAILS THANK YOU

SPSS for biologists: Kaplan Meier Survival Analysis using IBM Statistics KAPLAN MEIER PLOT Kaplan-Meier curves are widely used in clinical and fundamental research.It is also called Kaplan-Meier estimator or the product limit estimator(a non parametric statistics). It involves the calculation of the probability of each event at the time it occurs. It shows probability of an event for example survival rate is at certain time interval. If the sample size is large enough, the curve should approach the true survival function for the population under investigation. HOW TO PERFORM KAPLAN MEIER SURVIVAL ANALYSIS? In this tutorial we have showed the dataset of the patients having the information about their disease and how this information(like expression of the genes) is affecting the survival rate ? For more details please watch the video THANK YOU

Understanding the Importance of MANN WHITNEY and KRUSKAL WALLIS TEST MANN-WHITNEY U TEST : The Mann-Whitney U test is used to compare  the differences between two independent groups when the dependent variable is either continuous, but not normally distributed.   KRUSKAL WALLIS TEST: An extension of Mann Whitney U test  to allow the comparison of more than two independent groups is Kruskal Wallis Test. The Kruskal-Wallis H test is a  non parametric test. It can be used to determine if there are st atistically significant differences between two or more groups of an independent variable on a dependent variable. HOW BOTH TESTS ARE HELPFUL FOR A BIOLOGIST? In this video we have explained how to perform Mann-Whitney and Kruskal Tests and what are the differences between them? As in the previous video we perform Exact Fisher test in which we cannot use continuous values,both the tests are the alternative for that.We have the data of Cance...

EXPECTED OUTCOME OF COVID 19 USING FORECASTING ANALYSIS Forecasting is basically a statistical approach to make predictions for  the future on the basis of past or present observation.In biological terms, this approach is quite beneficial for the researchers to give predictions about any pandemic situation on the basis on previous knowledge/observation. For instance,We can calculate the substantial number of the patients that are going to be affected using Forecasting Analysis. AIM OF THIS TUTORIAL In this tutorial we try to explain about the current COVID 19 Pandemic situation respectively in Pakistan.We have the corresponding data about the patients per million for 4 weeks.On this basis ,we have predicted the increase in numbers for next 7 days by applying forecasting Analysis For more details about how to do Forecasting Analysis watch the video THANK YOU!!

SPSS FOR BIOLOGISTS:WHAT IS PEARSON CORRELATION COEFFICIENT? The most common measure of correlation in stats is the Pearson Correlation. The full name is the Pearson Product Moment Correlation (PPMC).It is a test statistics that measures the statistical relationship, or association, between two continuous variables and shows the linear relationship between them. WHAT ARE THE POSSIBILITIES? A correlation coefficient of 1 means that for every positive increase in one variable, there is a positive increase of a fixed proportion in the other. A correlation coefficient of -1 means that for every positive increase in one variable, there is a negative decrease of a fixed proportion in the other. Zero means that for every increase, there isn’t a positive or negative increase.In simple words "no correlation". AIM OF THIS TUTORIAL? In this video, we try to explain about how to find out the correlation between different gene expressions of a patient sample.This wa...

SPSS for Biologists: How to perform basic Fisher's or Chi-square test? SPSS (Statistical package for the social sciences) is the set of software programs that are combined together in a single package. This data can be mainly used for                                 Interestingly, the 21st century is becoming testing times for all basic researchers who are not equipped with dealing the big data. These terms, data science or big data, look extremely challenging to researchers specially to biologists.  Aim of Tutorials The aim of making these tutorials is to help the biologists to improve   their skills to deal with large amount of biological data. The first and the most  basic is how to use of Chi Square test/Exact Fisher  Test. CHI Square Test                             ...