PROTEIN BIOINFORMATICS

An Algorithmic Approach to Sequence and Structure Analysis

Ingvar Eidhammer, Inge Jonassen, William R. Taylor

Computer programs

• Chapter 1 - Pairwise Global Alignment of Sequences
  • EMBOSS
• Chapter 2 - Pairwise Local Alignment and Database Search
  • Dot matrices
    • Dotter
    • dotmat
  • Alignment programs
    • EMBOSS
  • Data base search programs
    • MPsrch (Smith and Waterman)
    • ScanPS (Smith and Waterman)
    • WU-BLAST
    • NCBI BLAST
    • PSI Blast
    • EBI Fasta
• Chapter 4 - Multiple Global Alignment and Phylogenetic Trees
  • Multiple alignment
    • ClustalW
    • ClustalX
    • MAP
    • Dialign
    • DCA
    • TCoffee
    • MAFFT
    • IBM-Tmsa
  • Phylogeny
    • Program list
    • PHYLIP
    • UCMP
    • Programs
• Chapter 6 - Profiles
  • Profile
    • PROFILEWEIGHT
    • ARIADNE
    • PFTOOLS
  • HMM profiles
    • HMMER
• Chapter 7 - Sequence Patterns
  • Pattern discovery
    • Pratt
    • IBM-Tad
    • Tspd
    • MEME
    • Teiresias
• Chapter 8 - Structure and Structure Description
  • PDB
  • DSSP-Nijmegen
  • DSSP-Pasteur
• Chapter 9 - Superposition and Dynamic Programming
  • PCSB
• Chapter 10 - 11 Structure Comparison
  • BioInfo3D