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Next: Bibliography Up: Bioinformatics Tutorial Previous: Molecular phylogenetic tree.

Other bioinformatics tools

So far in this tutorial, you have made use of only a small selection of bioinformatics techniques and tools. In the last exercise we invite you to explore additional tools and resources by yourself. Results of aligning sequences can be improved by systematically building up profiles from multiple sequences.

Tools, resources, and link collections:




ClustalW (http://bioweb.pasteur.fr/seqanal/interfaces/clustalw.html)
Perform a multi-sequence or profile-profile alignment with the program ClustalW. Just access the website directly and paste in all or a selection of your Class II tRNA synthetases in order to execute the program. ClustalW is the most widely used tool in bioinformatics for carrying out multi-sequence alignments.

Psipred (http://bioinf.cs.ucl.ac.uk/psiform.html)
Predict the secondary structure of one of your Class II tRNA synthetases with the Psipred Protein Structure Prediction Server. Paste your sequence in the input sequence window, provide your email address and you will receive after a few minutes a secondary structure prediction of your chosen tRNA synthetase. Sequence and structural alignments as well as secondary predictions form the framework for a successful modeling project.

3D PSSM (http://www.sbg.bio.ic.ac.uk/~3dpssm/)
A web-based method method for protein fold recognition using sequence profiles coupled with secondary structure.

TMpred (http://www.ch.embnet.org/software/TMPRED_form.html)
A database scoring-based method to predict the transmembrane portions of membrane proteins.

TMHMM (http://www.cbs.dtu.dk/services/TMHMM-2.0/)
A hidden Markov method to predict the transmembrane portions of membrane proteins.

European Bioinformatics Inst. (http://www.ebi.ac.uk/services/index.html)
An up-to-date and well-organized collection of links to bioinformatics tools, databases, and resources. The site provides advice as to the best or most popular tools in a category, and provides short descriptions of all entries.

ExPASy Molecular Biology Server (http://ca.expasy.org/)
Another well-organized directory of online analysis tools, databases, and other resources, with a greater focus on proteins. ``The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures...'' With this server you can start your own homology modeling project of an unknown class II tRNA synthetase, namely Alanyl-tRNA synthetase. You can obtain the sequence in FASTA format from the SwissProt database which can be accessed directly from the ExPASy server with the accession number SYA_ECOLI. As structural template choose one of the provided catalytic domain structures of class II tRNA synthetases. You can also model the other domains for which you need to find an appropriate template from the provided PDB structures.

SwissModel (http://swissmodel.expasy.org/)
For model generation use SwissModel, where you can thread your sequence upon one or several of your chosen templates. SwissModel provides you with an on-line tutorial and will perform refinements on initial models you submit to its server.

Dynamic Programming in Java
(http://www.dkfz-heidelberg.de/tbi/bioinfo/PracticalSection/AliApplet/index.html)

This is an alternative Smith-Waterman tutorial which will provide you with a web-based interface for dynamic programming, an animated version of the paper-and-pencil exercise in section 5.

Biology WorkBench (http://workbench.sdsc.edu)
This website allows you to search popular protein and nucleic acid sequence databases. Sequence retrieval is integrated with access to a variety of analysis tools as for example the multi-sequence alignment program ClustalW. The advantage of the Biology Workbench is that all analysis tools are interconnected with each other eliminating the tedious file conversion process, which often needs to be done when accessing tools from distinct locations.

CASP5 (http://predictioncenter.llnl.gov/casp5/Casp5.html)
Every two years a community-wide protein structure prediction contest takes place,where groups complete for prediction of unpublished protein structures. One can check out how well has our Resource done in the last year contest. Just search for Zan Schulten Group results on this site.


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Next: Bibliography Up: Bioinformatics Tutorial Previous: Molecular phylogenetic tree.
zan@uiuc.edu