Summary on Multiple Alignment Resources on the WWW

Georg Fuellen fuellen at techfak.uni-bielefeld.de
Tue Mar 7 06:58:23 EST 1995


The summary can be found below !

First, let me try to locate the following 4 resources _on the WWW_:

1. The ATLAS interface to sequence data, by which you can retrieve
   a sequence using a suitable subsequence of only a few amino acids.

2. McClure's Multiple Alignment Data (they are supposed to be at
   ftp.embl-heidelberg.de, according to the EMBL File Server News, Number 11,
   but I could not find them).

3. Kececioglu's maximum weight trace data, Reference:
   J. D. Kececioglu, The maximum weight trace problem in multiple sequence
   alignment. In Proc. of the 4th Symp. on Comb. Pattern Matching, LNCS 684,
   pp. 106-119 (1993)

4. A _pairwise_ alignment WWW Form. (Plain & simple, eh ? :-)

Now here's the summary. Thanks to all who responded; in particular
Peter De Rijk, Fredj Tekaia, Reinhard Schneider, Liisa Holm, Richard Hughey.
and Martin Leach.

PLEASE REPORT ANY USEFUL RESOURCES THAT ARE NOT ON THIS LIST !!!!!

Analysis of Multiple Alignments :
=================================

http://geoff.biop.ox.ac.uk/servers/amas_server.html
AMAS - Analyse Multiply Aligned Sequences

http://www.bio.cam.ac.uk/cgi-bin/seqlogo/logo.cgi
WebLogo Sequence Logo Generation Main Form

Calculation of Multiple Alignments :
====================================

http://ibc.wustl.edu/msa.html
MSA, Calcutating Multiple Alignments.

http://ibc.wustl.edu/msa/clustal.cgi
CLUSTALW Multiple Sequence Alignments, UNDER CONSTRCUTION

http://cbrg.inf.ethz.ch/subsection3_1_1.html#SECTION0001100000000000000
AllAll: Calculate Phylogenetic Trees, Alignments and a lot more

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

Explanatory texts:
==================

http://geoff.biop.ox.ac.uk/papers/rev93_1/rev93_1.html
Protein Sequence Alignment and Database Scanning, by Geoffrey Barton

http://www2.pasteur.fr/~tekaia/MAcours/multalign.html
Multiple Sequence Alignments, by Fredj Tekaia, UNDER CONSTRCUTION

http://lenti.med.umn.edu/MolBio_man/MolBio_man.html
AGRENET's GCG-oriented tutorial

Databases:
==========

http://www.embl-heidelberg.de/srs/srsc?-info||ALI
3D-ALI Database Interface; structurally verified alignments
gopher://s-crim1.dl.ac.uk/00/EMBnet%20Bioinformation%20Resource%20UK/Data%20%26%
20Software/databases/3d_ali/3d_ali.doc
3D-Ali Information File

http://www.sander.embl-heidelberg.de/fssp/paper.html
FSSP database of structurally aligned protein fold families

Software packages:
==================

gopher://megasun.bch.umontreal.ca/11/CMB/
Various 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)

Other:
======

http://kiwi.bcm.tmc.edu:8088/search-launcher/launcher.html
A WWW search launcher for Biologists. Multiple Alignment section:
UNDER CONSTRCUTION

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


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
    Dr Stephen R Covey, The 7 Habits of Highly Effective People, Habit #2:
    Begin With The End In Mind !
For info about a free online Biocomputing Course, to be offered in Summer 1995
under the auspices of GNA-VSNS, please point your WWW/hypertext browser to
http://www.techfak.uni-bielefeld.de/techfak/persons/fuellen/BCDhome.html
Please visit this page before inquiring about the course !





More information about the Bio-soft mailing list