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.

Basic Local Alignment Search Tool (BLAST) is a collection of programs developed using heuristic algorithm in C++ for comparing DNA, RNA, and protein sequences. The standalone command-line interface (CLI) of BLAST is named as BLAST+. The latest version of NCBI BLAST+ can be downloaded from the FTP server of NCBI ( ftp://ftp.ncbi.nih.gov/blast/executables/blast+/LATEST ). This is a simple tutorial for creating a custom database, accessing the database, and performing a sequence search using BLAST+. 1. Creating a Custom Database A nucleotide ( nucl ) or protein ( prot ) database can be created using -dbtype parameter in makeblastdb program. We can create two types of database using command-line below, Non-indexed Database: ./makeblastdb -in DBX.fasta -out DBX -dbtype prot Building a new DB, current time: 12/04/2020 10:10:06 New DB name: C:\NCBI\blast-2.6.0+\bin\DBX New DB title: DBX.fasta Sequence type: Protein Keep MBits: T Maximum file size: 1000000000B Adding sequences ...