Day 1

1.1 Sequence analysis, homology

Files for practical part:
1-1.fasta / seq1.fasta / seq2.fasta / seq3.fasta

Links:
http://blast.ncbi.nlm.nih.gov/Blast.cgi
http://www.uniprot.org/blast/

1.2 Multiple sequence alignments

Files for practical part:
2-1.fasta / 2-2.fasta / result3_fasta

Links:
http://www.ebi.ac.uk/Tools/msa/tcoffee/
http://www.uniprot.org/uniprot/P07998

1.3. Phylogenetic analyses

Files for practical part:
3-1.fasta / seq4.fasta / seq5.fasta / seq6.fasta

Links:
http://www.trex.uqam.ca/
http://www.ebi.ac.uk/Tools/msa/tcoffee/

1.4. Protein structure, Chimera

1.5. Protein domains

Links:
http://pfam.xfam.org

 

Day 2

2.1. Secondary structure

Files for practical part: MR1_fasta / glul_fasta / glul_aln

Links:
http://www.jalview.org
http://www.ncbi.nlm.nih.gov/gene
http://www.compbio.dundee.ac.uk/jpred4

2.2. Structure modeling by homology

Links:
http://aquaria.ws
http://aquaria.ws/Q9HD67/
http://genetics.bwh.harvard.edu/pph2

2.3. Protein feature prediction

Files for practical part:littleMSA_fasta / ferredoxins2_fasta

Links:
http://www.uniprot.org/uniprot/Q28WW9
http://www.uniprot.org/uniprot/Q28WW9.fasta
http://www.cbs.dtu.dk/services/TMHMM

2.4. Composition bias and repeats

Files for practical part: MR1_fasta / littleMSA_fasta

Links:
http://myhits.isb-sib.ch/cgi-bin/dotlet
http://matthuska.github.io/biasviz/