IN4173 / MCB

Delft - Leiden BioInformatics Master track »

Molecular Computational Biology 2009

A.P. Gultyaev (Sacha)
Instituut voor Biologie Leiden (IBL)
a.p.gultyaev (a) biology.leidenuniv.nl

H.J. Hoogeboom (Hendrik Jan) »
Institute for Advanced Computer Science (LIACS)
hoogeboom (a) liacs.nl

Schedule: Tuesday Feb 3 - Apr 28, 9.00-10.45, Snellius 174.
classes

Exam: 2 June 2009, 14.00-17.00, Snellius 174
To practise: old exams.

Schedule

Recommended reading and websites

Altschul S.F. et al.

The statistics of sequence similarity scores. (BLAST tutorial). www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html

Brudno M. et al. (2003).

LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13:721-731.
doi: 10.1101/gr.926603 (free full-text at www.genome.org)

Durbin R., Eddy S.R., Krogh A., Mitchison G. added (HJH)

Biological Sequence Analysis, Cambridge University Press, 1998. (see e.g., amazon.co.uk)

Eddy S.R. (2004a).

What is dynamic programming? Nature Biotechnology 22:909-910
(doi: 10.1038/nbt0704-909)

Eddy S.R. (2004b).

Where did the BLOSUM62 alignment score matrix come from? Nature Biotechnology 22:1035-1036.
(doi: 10.1038/nbt0804-1035)

Eddy S.R. (2004c). added (HJH)

What is a hidden Markov model? Nature Biotechnology 22:1315-1216
(doi: 10.1038/nbt1004-1315)
This and other introductions to Computational Biology, as Primer in Nature Biotechnology.

Gribskov M., McLachlan A.D. & Eisenberg D. (1987).

Profile analysis: detection of distantly related proteins. Proc. Natl. Acad. Sci. USA 84:4355-4358.
(PMCID: 305087)

Pearson W.R. & Lipman D.J. (1988).

Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85:2444-2448.
(PMCID: 280013)

Sippl M.J. (1993).

Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures. Journal of Computer-Aided Molecular Design 7:473-501. www.came.sbg.ac.at/Publications/JCAMD.7-473-501.pdf

Schwartz S. et al. (2003).

Human-mouse alignments with BLASTZ. Genome Res. 13:103-107.
doi: 10.1101/gr.809403 (free full-text at www.genome.org)

Thompson J.D., Higgins D.G. & Gibson T.J. (1994).

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
(PMCID: 308517)

Zuker M. (2000).

Calculating nucleic acid secondary structure. Curr. Opinion Struct. Biol. 10:303-310. doi: 10.1016/S0959-440X(00)00088-9 (within University free under Elsevier contract)

WWW

Database	Function	Organization	Address
GenBank	Nucleotide	National Center for Biotechnology Information	www.ncbi.nlm.nih.gov BLAST!
	search ENTREZ for:
EMBL	Nucleotide	European Bioinformatics Institute	www.ebi.ac.uk
SWISSPROT	Amino acid	Swiss Institute of Bioinformatics	www.expasy.org
	ExPASy (Expert Protein Analysis System) proteomics server
PSIPRED	Protein structure		www.psipred.net
	Protein Structure Prediction Server
MFOLD	RNA structure	Bioinformatics Center at Rensselaer and Wadsworth	www.bioinfo.rpi.edu/applications/mfold

Some other addresses from the lecture notes:

Section 1.1: Sample GenBank Record

Section 5.2.1: For instance, SWISS-MODEL, one of the first servers for protein structure predictions, initiated in 1993 and accessible via the ExPASy web server. (swissmodel.expasy.org)

Section 6.1: Many of these parameters have been estimated from thermodynamic experiments (e.g. D.Turner et al.) and are available in the Internet. frontend.bioinfo.rpi.edu/zukerm/rna/energy/

The algorithm used for energy minimization by dynamic programming is somewhat similar to the algorithm used for alignment problem. The program mfold (M. Zuker) is the most frequently used. Mfold web server: www.bioinfo.rpi.edu/applications/mfold

Section 6.2: Kinefold server of H. Isambert allows one to visualise kinetics of RNA folding. kinefold.u-strasbg.fr

Section 6.4: An example of user-friendly server is GPRM (genetic programming for RNA motifs) server (Hu, 2003). (bioinfo.cis.nctu.edu.tw/service/gprm).

Exercises/assignments 2009

To avoid tedious re-typing of the sequences, we made the assignments available on the web.