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...the script <code>run.pl</code> here on biocluster: <code>/mnt/home/student/kalemanovm/master_practical/Assignment2_Alignments/scripts/task1</code>. The usage of #example usages: ( from directory /mnt/home/student/kalemanovm/master_practical/Assignment2_Alignments/output/task1, but please do not try

...t <code>parse_output.pl</code> here on biocluster: <code>/mnt/home/student/kalemanovm/master_practical/Assignment2_Alignments/scripts/task1</code> or just copy t my $pdb70clusters_file = "/mnt/home/student/kalemanovm/master_practical/Assignment2_Alignments/scripts/task1/pdb70clusters.txt";

.../code> and all intermediate and resulting files in <code>/mnt/home/student/kalemanovm/master_practical/Assignment2_Alignments/results/task1</code>.

...lue using R. You can find the script here on biocluster: /mnt/home/student/kalemanovm/master_practical/Assignment2_Alignments/scripts/task1 or just copy the code

...or all parameters are summarized can be seen here: <code>/mnt/home/student/kalemanovm/master_practical/Assignment3_SequenceBasedPredictions/SecondaryStructure/re Other used scripts and created data can be found in: /mnt/home/student/kalemanovm/master_practical/Assignment3_SequenceBasedPredictions/SecondaryStructure.

The alignment is located here on the student server: <code>/mnt/home/student/kalemanovm/master_practical/Assignment6_Evolutionary_sequence_variation/pfam_Ras_ali/r The alignment is located here on the student server: <code>/mnt/home/student/kalemanovm/master_practical/Assignment6_Evolutionary_sequence_variation/pfam_Glyco_hyd

-i /mnt/home/student/kalemanovm/master_practical/Assignment2_Alignments/output/task1/hhblits-2iter-uniprot2 -ts /mnt/home/student/kalemanovm/master_practical/Assignment4_StructuralAlignments/hhmakemodel/P04062_models

perl /mnt/home/student/kalemanovm/master_practical/Assignment2_Alignments/scripts/task1/parse_output.pl --out perl /mnt/home/student/kalemanovm/master_practical/Assignment2_Alignments/scripts/task1/devide_psiblast_out.p