DNA Multiple Sequence Alignment

[Georg Fuellen]

Janine Graves wrote:
> I'm a mathematician just starting to look at multiple sequence alignment
> of DNA.  I'm not very familiar with the field and seek references on
> algorithms or survey articles on this subject.

A couple of resources, including a tutorial I wrote for an online course, are
listed at http://www.techfak.uni-bielefeld.de/bcd/Curric/MulAli/welcome.html
I'd like to take the chance to append the list (below), and ask everyone
to please MAIL ME ADDITIONS, CORRECTIONS, etc. I'll update the list, and the
newest version will be kept available at the URL above, and its mirrors at
http://www.biotech.ist.unige.it/bcd/Curric/MulAli/welcome.html
http://merlin.mbcr.bcm.tmc.edu:8001/bcd/MulAli/Curric/welcome.html

Also, if anyone is interested to test beta Perl code for handling multiple
alignments, please drop me a note !


Multiple Alignment Internet Resource Summary
============================================
           Thanks to Christian Frosch for his help in maintaining this list !

Analysis of Multiple Alignments :

http://geoff.biop.ox.ac.uk/servers/amas_server.html
AMAS - Analyse Multiply Aligned Sequences 
Visualization of physico-chemical properties of the columns of an alignment

http://www.bio.cam.ac.uk/cgi-bin/seqlogo/logo.cgi
WebLogo Sequence Logo Generation Main Form
Visualization of the conservation (and more!) of the columns of an alignment

Calculation of Multiple Alignments on the WWW :

(Most Fill-Out Forms include a link to the software itself, e.g.
ClustalW, MSA, and ToPLign) 

(UPDATED Feb 6) http://dot.imgen.bcm.tmc.edu:9331/multi-align/multi-align.html
Baylor's search launcher for Biologists, Multiple Alignment section
ClustalW, MAP, PIMA 1.4, MSA 2.1, and BLOCK MAKER alignments

(UPDATED Feb 6) http://adenine.bchs.uh.edu/multi-align/multi-align.html
This site now seems to be a mirror of the above.

http://cartan.gmd.de/ToPLign.html
ToPLign: Toolbox for Protein Alignment
Computing, analysis and visualization of pairwise, multiple, threading, 
and parametric alignments. 

http://ibc.wustl.edu/msa.html
MSA, (Close-to-) Optimal Alignments using the Carrillo-Lipman bound

http://cbrg.inf.ethz.ch/subsection3_1_1.html
AllAll: Calculate Phylogenetic Trees, Alignments, dSplits, Probabilistic 
ancestral sequence, {Kabat-Wu, probability, maximum likelihood} variation index, 
prediction of Surface/Interior/Active site, prediction of parse regions.

http://www.embl-heidelberg.de/predictprotein/predictprotein.html
MaxHom Alignments (offered together w/ structure prediction)
Info: http://www.embl-heidelberg.de/predictprotein/phd_help.html#P3PIR

http://www.cse.ucsc.edu/research/compbio/sam.html
SAM: Sequence Alignment and Modeling.
Hidden Markov model multiple alignment and discrimination.

http://genome1.bio.bnl.gov/cgi-bin/bbq?para=mra.bbq&MODE=0
MRA, Alignment for Many Sequences by Comparison of Dot-matrices. 

http://www.genebee.msu.su/services/malign_reduced.html
GeneBee Multiple alignment: pairwise motifs -> multiple motifs -> "supermotifs" 
-> construction of multiple alignment. 

Databases:

http://www.techfak.uni-bielefeld.de/bcd/Curric/MulAli/databanks.html
Collection of Databanks relevant to Multiple Alignment
3d-Ali, ALIGN/PRINTS, FSSP, HSSP, PIRALN, GCRDb/TM7, HHS

Tutorial texts:

http://geoff.biop.ox.ac.uk/papers/rev93_1/rev93_1.html
Protein Sequence Alignment and Database Scanning, by Geoffrey Barton
ca. 30 pages text, 10 figures.

http://www.techfak.uni-bielefeld.de/bcd/Curric/MulAli/mulali.html
A Gentle Guide to Multiple Alignment, by Georg Fuellen
ca. 50 pages text, ca. 20 figures, exercises, solution sheet.
A lot of the resources mentioned here are treated in detail in part 3.3,
e.g. MSA/Clustal and, by way of exercises, AMAS and WebLogo. 

http://www2.pasteur.fr/~tekaia/MAcours/multalign.html
Multiple Sequence Alignments, by Fredj Tekaia, 
ca. 5 pages text

http://www2.pasteur.fr/~tekaia/MAcours/clustalw.html
ClustalW tutorial, by Fredj Tekaia.
ca. 5 pages text

http://biotech.bio.tcd.ie/acerhelp/ClustalW-Acerhelp.RTF.txt.html
ClustalW tutorial, Andrew T. Lloyd
ca. 5 pages text

http://lenti.med.umn.edu/MolBio_man/MolBio_man.html
AGRENET's Unofficial Guide to GCG Software
ca. 50 pages text

NEW Feb 26 http://www.dl.ac.uk/embnet.news/vol2_1/align.html
A short introduction to algorithms for multiple sequence alignments
ca. 4 pages text

Software packages:

(Some software packages offer a Fill-Out Form for doing calculations 
by way of a WWW server; they are listed above, e.g. Clustal, MSA, and ToPLign.) 

http://www.ebi.ac.uk/biocat/biocat_algt.html
BioCatalog, Section on (Multiple) Alignment search software, editing 
and display, and browsers.

http://www.icot.or.jp/ICOT/IFS/IFS-abst/ifs-catalogue.html
Various software packages (No. 55,56,75,76,93-95) running on parallel computers
Dynamic Programming, Simulated Annealing, Genetic Algorithm, Iterative 
Improvement, Intelligent Refinement, RNA-Sequence Considering Stem Regions.

gopher://megasun.bch.umontreal.ca/11/CMB/
Starter page for various software packages 
MEGA, GDE, Phylip, etc

(UPDATED May 22) http://genome.wustl.edu/eddy/hmmer.html
HMMER -- Hidden Markov model software "to do multiple sequence alignment and very
sensitive database searching". 

(UPDATED Feb 6) ftp://juno.ucsd.edu/progs
Programs for progressive alignment (Feng & Doolittle) of protein sequences 
and the construction of phylogenetic trees from them. (See file readme.doc) 

http://indigo2.uia.ac.be:80/~peter/dcse/
DCSE (Dedicated Comparative Sequence Editor)

ftp://morgan.angis.su.oz.au/pub/unix
ShadyBox is a drawing program which enables you to box and shade regular
and irregular shaped segments of aligned multiple sequences.

Other:

http://www.cs.monash.edu.au/~lloyd/tildeStrings/index.html
DNA multiple alignment programs, Tech Reports, Bibliography. 

http://www.blocks.fhcrc.org/
BLOCKS WWW Server
Detection and verification of protein sequence homology


---
best wishes,
  georg
fuellen at dali.Mathematik.Uni-Bielefeld.DE, fuellen at MIT.EDU
  http://www.techfak.uni-bielefeld.de/techfak/persons/fuellen/georgF.html