BioGem Blog

UPGMA (Unweighted Pair Group Method with Arithmetic Mean) is a distance-based method for constructing phylogenetic trees. It works by iteratively clustering the two closest groups of sequences together, forming a new cluster until all sequences are grouped into a single tree. The distances between clusters are calculated using the average of all pairwise distances between sequences within those clusters. UPGMA produces rooted trees, meaning it has a defined root representing the common ancestor. Here's a more detailed explanation: 1. Distance Matrix UPGMA begins with a distance matrix, which contains the pairwise distances between all sequences being compared. These distances can be based on sequence alignment, protein structure comparisons, or other relevant metrics. \[D_{i,j}=\max\begin{cases}D_{i-1,j-1} & + & s(a_i,b_j) \\D_{i-1,j} & + & s(a_i,-) \\D_{i,j-1} & + & s(-,b_j)\end{cases}=\max\begin{cases}D_{i-1,j-1}& + ...

BioEdit is a free biological sequence alignment editor. It has an intuitive multiple document interface and offers convenient features that make alignment and manipulation of sequences relatively easy on windows desktop computers. Additionally, there are several sequence manipulation and analysis options and links to external analysis programs that facilitate a working environment, allowing users to view and manipulate sequences with simple point-and-click operations. The BioEdit software provides automated local and web BLAST ( B asic L ocal A lignment S earch T ool) searches with a simple graphical user interface (GUI) to the command-line BLAST program. This is a simple video tutorial on how to construct a custom nucleotide/protein database using BioEdit software to support NCBI BLAST . The tutorial also covers how to perform a query search, specifically pairwise sequence alignment, against the database.

A phylogenetic tree ( a.k.a. , cladogram or dendrogram) is a diagrammatic/graphical representation of the genetical/evolutionary relationship of species/organisms/genes. It helps to find the common ancestor. Construction of a phylogenetic tree consists of two phases, multiple sequence alignment and computing distance matrix. This is a simple video tutorial for constructing a phylogenetic tree using Molecular Evolutionary Genetics Analysis ( MEGA ) software. The MEGA software produces phylogenetic trees from multiple sequences in various formats: rectangular, slanting, curved, radial, and curved.

This is a simple tutorial which explains how to design your own web interface for NCBI BLAST+ to perform local and online database search using PHP in webserver. The PHP library loc BLAST executes the NCBI BLAST+ programs using exec() function through passing parameters from the HTML form fields. In loc BLAST , two list boxes were used to select program & database, and text area & file upload is used to input query sequence in the FASTA file format. A FASTA file validation function is included to validate the query sequence before executing the BLAST programs. The loc BLAST PHP library and test database files were freely available at GitHub . Requirements for loc BLAST Setup In this tutorial, I have given a brief explanation about embedding the latest NCBI BLAST+ (the latest version of NCBI BLAST+ as on November 17, 2020 is 2.11.0 .) in any PHP enabled web server. The latest version of NCBI BLAST+ (standalone command-line BLAST programs) can be downloaded from the FTP s...