Biochemistry and Molecular Biology Subject Guide

BLAST is a program that finds areas of similarity in nucleotide and protein sequences. In addition to the application, there is a good web based version.

Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI’s Entrez retrieval service. Cn3D runs on Windows, Macintosh and Unix. Cn3D simultaneously displays structure, sequence and alignment, and now has powerful annotation and alignment editing features

Expasy is the bioinformatics resource portal of the SIB Swiss Institute of Bioinformatics.
It is an extensible and integrative portal which provides access to over 160 databases and software tools, developed by SIB Groups and supporting a range of life science and clinical research domains, from genomics, proteomics and structural biology, to evolution and phylogeny, systems biology and medical chemistry.

The NCBI Genome Data Viewer (GDV) is a genome browser supporting the exploration and analysis of annotated eukaryotic genome assemblies. The GDV browser can visualize different types of molecular data in a whole genome context, including gene annotation, BLAST alignments, and experimental study data from the NCBI GEO and dbGaP databases. GDV release notes describe new features relating to this browser.

PyMOL is a widely used open-source molecular visualization system.