Algorithmic Bioinformatics - BIOTEC - Biotechnology Center TU ...

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2 Οκτ 2013 (πριν από 3 χρόνια και 8 μήνες)

80 εμφανίσεις

Michael Schroeder



BioTechnological Center

TU Dresden

Biotec

Algorithmic Bioinformatics

By Michael Schroeder, Biotec






2

Bioinformatics cycle


Applied bioinformatics


Use bioinformatics tools


Access databases and tools over the web


Programming for bioinformatics


Learn programming skills relevant to bioinformatics


Algorithmic bioinformatics


Develop bioinformatics tools


By Michael Schroeder, Biotec






3

Syllabus


The module covers
algorithms and data structures for
bioinformatics
. It will cover:


sequences (DNA and amino acid sequences).


structure (structure comparison and alignment)



For each of these data types the module will cover important
algorithms to manipulate and analyse the data.





Students will appreciate the
different types of data
mostly generated
in bioinformatics


Students will understand how to
analyse the different types of data


Students will be able to
design data structures and algorithms
to
analysis bioinformatics data


Students will be able to critically
assess quality of algorithms


Students will be able to
write basic programmes

By Michael Schroeder, Biotec






4

Book


Protein Bioinformatics by
Eidhammer et al.


Chapters on


sequence alignment,


multiple sequence
alignment, and


structure alignment

By Michael Schroeder, Biotec






5

Structure of module


Algorithms for Sequences


Sequence comparison


Multiple sequence alignment


Algorithms for Structures


Intro to structures


Superposition


Geometric techniques


Clustering


Advanced topics


Scoppi and Interaction interfaces


HMM and prediction of interactions


Structure prediction


Docking


Atomic force microscopy and bioinformatics


Textmining


Revision


Good news: Conceptually

You know most of the topics

We will cover

Bad news: It’s a long way

to understand all the details

By Michael Schroeder, Biotec






6

Labs


Annalisa and Frank will run the labs.


If you have any questions then contact him on:


Frank.dressel@biotec.tu
-
dresden.de



Style


Programming,


paper and pencil,


use programmes



By Michael Schroeder, Biotec






7

Lab Contents



Local and global sequence alignments


Phylogeny and clustering


Finding and highlighting sequence motifs in PDB
structures


Distance plots for inter
-
atomic distances



(Using programmes for docking, molecular modelling,
gene expression data analysis, textmining)


By Michael Schroeder, Biotec






8

Assessment


Lecture: Exam, which counts 80%


Lab:


Programming task in pairs 20%


Will be handed out during term

By Michael Schroeder, Biotec






9

Assessment


Homework is mandatory!



Each week you will be given tasks to complete for the
following week. You will not be marked on the
homework, but you must hand it in



Handing in of homework is pre
-
requisite for the
programming task



no homework = no marks

By Michael Schroeder, Biotec






10

Preparation for labs and lectures


Get Book


Read Book


Read all slides from term 1 again


Read all slides from term 2 again


Do all programming labs of term 2 again, especially


Dot plots


Sequence alignments


Residue counts