Multiple Alignment Resources on the WWW

Georg Fuellen fuellen at techfak.uni-bielefeld.de
Wed Nov 1 16:28:59 EST 1995


The following is the Multiple Alignment Resource Page
developed for the GNA-VSNS Biocomputing Course, see 
http://www.techfak.uni-bielefeld.de/bcd/welcome.html

This list, and any updates are available at:
http://www.techfak.uni-bielefeld.de/bcd/Curric/MulAli/welcome.html
http://merlin.mbcr.bcm.tmc.edu:8001/bcdusa/Curric/MulAli/welcome.html
http://info.mcc.ac.uk/hpctec/courses/Biocomputing/vsns/bcd/Curric/MulAli/welcome.html

PLEASE REPORT ANY USEFUL RESOURCES THAT ARE NOT ON THIS LIST !!!!!
Email them to fuellen at dali.mathematik.uni-bielefeld.de.
Also, please mail me corrections, updates, flames, etc !

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) 

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

http://adenine.bchs.uh.edu/multi-align/multi-align.html
Baylor/UH search launcher for Biologists, Multiple Alignment section
ClustalW, PIMA, MAP, BLOCK MAKER and TreeAlign alignments

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://ibc.wustl.edu/msa/clustal.cgi
CLUSTALW, Heuristic Multiple Alignments using Alignment Along a Tree

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://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, under construcution
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

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

http://www.cse.ucsc.edu/research/compbio/sam.html
SAM: Sequence Alignment and Modeling System

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.

(Thanks to the Molecular Biology Computational Resource at Baylor College Of 
Medicine, and the Manchester and North High Performance Computing Training 
and Education Centre (MAN T&EC) for mirroring assistance.)

--
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











More information about the Comp-bio mailing list