Practical Course: "Bioinformatics Software Tools"
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| General Subject: |
Practical informatics |
Tutors:
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Daniel Richter, Alexander Auch and Prof. D.
Huson
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Time:
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February 19 - March 02, 2007, 9:00-17:00
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Preliminary discussion:
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February 14th, 17:00 s.t., C311, Sand 14, AB Huson
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| Amount: |
4 SWS, examinable: 2 SWS |
| Location: |
Computer room C311
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Office hours:
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by appointment
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Enrolment:
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by eMail to Daniel Richter
with indication of complete name, matricle number and WSI login ID
Maximum number of participants: 9 |
| Description: |
In this tutorial we want to look at several software tools that are widely used
at the moment.
E.g.: Programs for sequence comparison (pairwise and multiple alignments,
e.g. ClustalW, T-Coffee, Muscle), programs for phylogenetic reconstruction
(e.g. Phylip, Paup, SplitsTree), database search (e.g. BLAST, HMMer),
visualization (e.g. CGViz), genome finishing, genefinding (e.g. genscan) and
others. |
Requirements for admission:
|
completed Vordiplom Bioinformatik, the lectures
"Algorithms in Bioinformatics I and II" are recommended.
Experiences with Java and at least one scripting language (Python, Perl, bash, ...) are needed. |
|
Course language
The teaching language is German or English if any participant does not
understand German.
For written documents (hand-outs, protocols etc.)
English is recommended.
| Day |
Exercises |
| 1 |
EMBOSS |
| 2 |
BLAST and visualization of sequence alignments |
| 3 |
MSA and Phylogeny |
| 4 |
Phylogeny |
| 5 |
Genome Assembly |
| 6 |
Annotierungs-Pipeline |
| 7 |
Annotierungs-Pipeline + WGP |
| 8 |
Metagenomics |
| 9 |
Support Vector Machines |
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