Dot Plot Analysis

     There are several programs in the EMBOSS suite, available through PISE.  They include Dotmatcher, Dottup, Dotpath, and Polydot.
     Dot plot analysis can also be performed at Dotlet, with customizable graphical output.  Dotter can be downloaded and installed on a local server.
     ImageBeat no longer has interactive utilities, but still has an interesting gallery.
     The DNA Learning Center provides a dotplot generator for sequences up to 200 characters, among other sequence utilities.

Dotplot at D�sseldorf

Sequence-to-Sequence Comparison

BLAST 2 Sequences allows the direct comparison of two sequences.  Details can be found in Tatusova & Madden (1999).

Dynamic Programming

A Flash-based illustration of dynamic programming might help you understand what's going on.

BLAST

     In order to decide which BLAST program to use, you can refer to NCBI's BLAST Program Descriptions for brief explanations.  However, the BLAST Program Selection Guide (available as a PDF) provides a decision tree to assist you in choosing the appropriate program.
     The BLAST Tutorial shows how to use the web interface, while the BLAST Course: The Statistics of Sequence Similarity Scores, written by Stephen Altschul, the developer of BLAST, explains scoring in detail.
     BLink Help explains NCBI's "BLAST Link" system, which displays pre-computed blastp searches for all proteins in Entrez Protein (GenPept).
     The initial version of BLAST is described in Altschul et al. 1990; the updated Gapped BLAST is covered in Altschul et al. 1997.

FASTA

     Descriptions of, and access to, individual FASTA programs can be found at U. Virginia (where it was developed), at PISE, and at EBI. Bill Pearson has some useful, though dated, information on Exploring Distant Protein Sequence Relationships.  For detailed descriptions of searching with FASTA, consult his Flexible sequence similarity searching with the FASTA3 program package.
     PRSS, which stands for Probability of Random Shuffle, is part of the FASTA suite and evaluates the significance of pairwise similarity scores using a Monte Carlo analysis. Similarity scores for the two sequences are calculated, and then the second sequence is shuffled 200 to 1000 times and compared with the first sequence.

PSI/PHI-BLAST

     One of this module's exercises is based on NCBI's PSI-BLAST Tutorial, focusing on a protein of unknown function from Methanococcus janaschii.
     PSI-BLAST is described Altschul et al. 1997, which also introduced Gapped BLAST.
     In order to use PHI-BLAST, you need to know PHI-BLAST Rules for pattern syntax to write effective queries.