Pairwise and Multiple Alignment
- Pairwise Sequence Alignment
- Robert Giegerich and David Wheeler
- Virtual School of Natural Sciences BioComputing Division (VSNS-BCD)
- Very thorough, highly mathematical, not for the novice.
- http://merlin.mbcr.bcm.tmc.edu:8001/bcd/Curric/PrwAli/
- Protein Sequence Alignment and Database Scanning
- Geoffrey J. Barton
- Laboratory of Molecular Biophysics, Univ. of Oxford, UK
- http://barton.ebi.ac.uk/papers/rev93_1/rev93_1.html
- Detailed and authoritative, but goes light on the
mathematics, understandable by the average scientist.
- [This is a preprint of the chapter in: Protein Structure prediction - a practical approach,
- Edited by M. J. E. Sternberg, IRL Press at Oxford University Press, 1996]
- Protein Sequence Alignment Techniques
- Geoffrey J. Barton
- EMBL/EBI, Cambridge, UK
- Excellent detailed discussion of alignment
techniques - satisfying level of analysis without overwhelming the
reader with equations.
- http://barton.ebi.ac.uk/papers/ccp4_98b/index.html
- [This is a preprint of a paper published in: (1998), Acta Cryst D54, 1139-1146]
- A Gentle Guide to Multiple Alignment
- Georg Fuellen, VSNS BioComputing Division
- Technical, mathematical, not so "gentle"
- http://merlin.mbcr.bcm.tmc.edu:8001/bcd/Curric/MulAli/mulali.html
- Algorithms For Multiple Sequence Alignments
- Guy Bottu, Belgian EMBNET Node (BEN)
- A short overview, well written, easy to understand.
- http://www.seqnet.dl.ac.uk/embnet.news/vol2_1/align.html
- CLUSTALW tutorial
- Fredj Tekaia, Institut Pasteur, France
- A set of exercises with step-by-step instructions
for using CLUSTALW, slightly annotated, but does not explain the theory
behind the program.
- http://www-alt.pasteur.fr/~tekaia/MAcours/clustalw.html
- SAM: Sequence Alignment and Modeling Software System - documentation
- Richard Hughey andAnders Krogh
- Baskin Center for Computer Engineering and Science
- University of California, Santa Cruz, CA
- Doucumentation for the authors' own HMM based
software with some general discussion of alignment issues.
- http://www.cse.ucsc.edu/research/compbio/papers/sam_doc/sam_doc.html