# WF Invocation UI BoF 1. Log in into https://usegalaxy.org 2. Import this history: https://usegalaxy.org/u/cartman/h/d3 3. Run this workflow: https://usegalaxy.org/u/cartman/w/wf-ui-bof 4. Look at invocation report and discuss it!
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Anton Nekrutenko
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Lecture 24: Sequence alignment

In the previous lecture we have seen the principle behind dynamic programming. This approach is extremely useful for comparing biological sequences, which is coincidentally one of the main points of this course. This lecture explain how this is done. In writing this text I heavily relied on wonderful course taught by Ben Langmead at Johns Hopkins. The cover image shows pairwise alignments for human, mouse, and dog KIF3 locus from Dubchak et al. 2000. How different are two sequences? Suppose you have two sequences of the same length: A C A T G C C T A A C T G C C T A C How different are they? In other words, how many bases should be change to turn one sequence onto the other: A C A T G C C T A

4/18/2024
Galaxy Outreach Style Guide

Colors

3/22/2024
Lecture 9: Python 5 - Processing files

Quiz Prep Go to https://colab.research.google.com Log in with your PSU account and create a new notebook Complete the quiz Share you notebook with aun1@psu.edu. Make sure you set me as an editor: Questions Question 1 (50 pts) Using a for loop write code that will calculate the sum of the numbers 1 through 100.

2/13/2024
Lecture 4: Intermission + History of Sequencing

The problem The difficulty with sequencing nucleic acids is nicely summarized by Hutchinson:2007: The chemical properties of different DNA molecules were so similar that it appeared difficult to separate them. The chain length of naturally occurring DNA molecules was much greater than for proteins and made complete sequencing seems unapproachable. The 20 amino acid residues found in proteins have widely varying properties that had proven useful in the separation of peptides. The existence of only four bases in DNA therefore seemed to make sequencing a more difficult problem for DNA than for protein. No base-specific DNAases were known. Protein sequencing had depended upon proteases that cleave adjacent to certain amino acids. It is therefore not surprising that protein-sequencing was developed before DNA sequencing by Sanger and Tuppy:1951.

1/22/2024
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