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Practical Course: "Software Tools for Computational Molecular
Biology", WS2003
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| Description: |
In this tutorial we want to look at several
software tools that are
widely used at the moment.
E.g.: Programs for sequence comarison (pairwise and multiple
alignments,
e.g. ClustalW, T-Coffee), programs for phylogenetic reconstruction
(e.g.
Phylip, Paup, SplitsTree), database search (e.g. BLAST, HMMer),
vizualisation
(e.g. CGViz), genefinding (e.g. genscan) and others. |
Requirements for admission:
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| completed Vordiplom Bioinformatik, the lectures
"Algorithms in Bioinformatics
I and II" are recommended. |
| Remark: |
The course has started, no further participants
may be admitted. |
|
Working material:
Session 22 Oct 2003: Sequence analysis with EMBOSS
pUC19.seq: sequence of a
cloning
vector in gcg format
Exercise: A study
of
a human protein
Listing of sessions with
protocols:
-
Sequence analysis with EMBOSS and study of a human protein
(Protocol by Kristoffer Forslund)
-
Introduction to phylogeny and the program package PAUP for
phylogenetic analysis (Protocol by Serhat Saydam)
-
Repeat detection with suffix trees using MUMmer,
application to detection of miRNAs in Arabidopsis (Protocol by Holger
Plattfaut)
-
miRNAs, continued (Protocol by Michael Remmert)
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Hidden Markov Models and HMMer (Protocol by Helge Florin)
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Geneprediction using Genscan (Protocol by Christian Mayer)
-
Introduction to Blast, theoretical and practical (Protocol
by Mathias Ganter)
-
Blast and visualization of genetic data with CGViz
(Protocol continued by Mathias Ganter)
-
Support Vector Machines (Protocol by Andreas Biegert)
All protocols in one pdf for
download
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Teaching