BioGem Blog

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.

The entropy in sequence analysis refers to the measure of the variation of characters (column) in multiple sequences. Entropy plot through multiple sequence alignment can be predicted using different types of entropy formulas, namely Shannon's Entropy , Schneider's Entropy , Shenkin's Entropy , Gerstein's Entropy , and Gap normalized Entropy . Prediction of entropy plot consists of two phases: ( i ) performing multiple sequence alignment and consensus, and ( ii ) calculation of entropy number for each column through consensus of multiple sequence alignment. The entropy plot is generated by plotting vertical lines in the order of the consensus sequence on the x -axis, and the entropy number on the y -axis. This simple video tutorial demonstrates how to predict entropy plot through multiple sequence alignment. The tools used in this tutorial are ClustalW , and Entropy Plotter . Note: We can choose any multiple sequence alignment tool, but the alignment output must...