https://cw.fel.cvut.cz/b172/ 2026-04-26T10:58:13+0200 https://cw.fel.cvut.cz/b172/ https://cw.fel.cvut.cz/b172/lib/tpl/bulma-cw/images/favicon.ico text/html 2018-02-28T11:03:40+0200 Anonymous (anonymous@undisclosed.example.com) https://cw.fel.cvut.cz/b172/courses/bin/tutorials/tutorial2?rev=1519812220&do=diff Tutorial 2 - de Bruijn and Overlap graphs, Velvet tutorial Problems TAATGCCATGGGATGTTk=3k=5TGGCAGCATTGCAATGCAATCAATTATTTGACk=4k=5 Practical Example In this tutorial, we are going to de-novo assembly a genome of an unknown organism. First, download the read data: text/html 2018-03-14T10:25:53+0200 Anonymous (anonymous@undisclosed.example.com) https://cw.fel.cvut.cz/b172/courses/bin/tutorials/tutorial3?rev=1521019553&do=diff Tutorial 3 - Sequence alignment, second assignment: SEQUENCE ALIGNMENT Problem 1 - score of an alignment Calculate the score of alignment PRT---------EINS YRNWPSEEN- Use BLOSUM62 scoring matrix and affine gap penalty with gap opening cost 11 and gap extension cost 1. gap opening penalty$\mathrm{gap\_penalty} = -4$$\mathrm{mismatch\_penalty} = -3$$\mathrm{match\_premium} = 5$$\lambda = 0.5$$5$$-3$$4$ text/html 2018-03-14T12:32:08+0200 Anonymous (anonymous@undisclosed.example.com) https://cw.fel.cvut.cz/b172/courses/bin/tutorials/tutorial4?rev=1521027128&do=diff Tutorial 4 - BLAST, Star Alignment, Clustal Omega Problem 1 - Multiple Sequence Alignment Score Calculate the score of the following alignment sum-of-pairs$+4$$-2$$-1$$s(\_,\_)=0$entropy $$\begin{array}{l} \mathtt{MQPILL\_G} \\ \mathtt{MLR\_LL\_G} \\ \mathtt{MK\_ILLL\_} \\ \mathtt{MPPVLLI\_} \end{array}$$ Calculate the consensus sequence. [Adapted from <http://www.bii.a-star.edu.sg/docs/education/lsm5192_04/Multiple%20Sequence%20Alignment%20Progressive%20Approaches.pdf>. ] Problem 2 - STAR … text/html 2018-04-11T19:42:40+0200 Anonymous (anonymous@undisclosed.example.com) https://cw.fel.cvut.cz/b172/courses/bin/tutorials/tutorial5?rev=1523468560&do=diff Tutorial 5 - UPGMA, Neighbor Joining Problem 1 - UPGMA Using UPGMA reconstruct the phylogenetic three that is consistent with the given data. Assume a set of sequences A = {a, b, c, d, e} and the corresponding distance matrix D. D a b text/html 2018-04-11T22:19:05+0200 Anonymous (anonymous@undisclosed.example.com) https://cw.fel.cvut.cz/b172/courses/bin/tutorials/tutorial6?rev=1523477945&do=diff Tutorial 6 - Parsimony - Fitch and Sankoff algorithms Problem 1 - Fitch's algorithm Based on the given structure of the phylogenetic tree, compute the total parsimony score using Hamming distance and determine internal nodes. Problem 2 - Sankoff's algorithm (weighted parsimony) text/html 2018-04-18T23:10:18+0200 Anonymous (anonymous@undisclosed.example.com) https://cw.fel.cvut.cz/b172/courses/bin/tutorials/tutorial9?rev=1524085818&do=diff Tutorial 9 - HMMER This tutorial follows the HMMER User’s Guide written by Sean R. Eddy, Travis J. Wheeler and the HMMER development team. Thanks. Problem 1 - Install HMMER First of all, we download HMMERv3.1b2 from <http://hmmer.org> and unpack it. wget http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2.tar.gz tar xfv hmmer-3.1b2.tar.gz cd hmmer-3.1b2