All public logs

Combined display of all available logs of 22111. You can narrow down the view by selecting a log type, the username (case-sensitive), or the affected page (also case-sensitive).

• 16:56, 18 September 2026 Carol talk contribs created page Exercise:BLAST new (Created page with "Exercise written by Carolina Barra Quaglia 2026 ==Introduction== In this exercise you will learn by doing to BLAST ('''B'''asic '''L'''ocal '''A'''lignment '''S'''earch '''T'''ool) DNA and protein sequences. After completion of the exercise you should be able to choose an appropriate BLAST search tool selecting the correct set of parameters, interpret a BLAST result, explain what an E-value means and how database size affects it, and decide what biological conclusion...")
• 19:52, 19 April 2026 Carol talk contribs created page Exercise:Unknown variant (Created page with " What happens when you don't find your variant of interest? As an example, we are going to work with a variant in glucagon-like peptide-1 receptor to assess whether patients bearing that mutation can respond to Ozempic ==Introduction== In this exercise, you will: Identify a mutation in a patient GLP1R sequence Determine its effect at the protein level Evaluate whether the mutation affects drug response (Ozempic) ===Tools you will use=== NCBI Nucleotide and GeneBank...")
• 14:01, 6 November 2025 Carol talk contribs created page File:GraphicSummary PSSM onPDB.png
• 14:01, 6 November 2025 Carol talk contribs uploaded File:GraphicSummary PSSM onPDB.png
• 14:01, 6 November 2025 Carol talk contribs created page File:PSSM-2 on PDB.png
• 14:01, 6 November 2025 Carol talk contribs uploaded File:PSSM-2 on PDB.png
• 13:06, 6 November 2025 Carol talk contribs created page File:Results PSI-BLAST iteration2.png
• 13:06, 6 November 2025 Carol talk contribs uploaded File:Results PSI-BLAST iteration2.png
• 12:45, 6 November 2025 Carol talk contribs created page File:GraphicSummary PB3.png
• 12:45, 6 November 2025 Carol talk contribs uploaded File:GraphicSummary PB3.png
• 12:45, 6 November 2025 Carol talk contribs created page File:Results PSI-BLAST iteration3.png
• 12:45, 6 November 2025 Carol talk contribs uploaded File:Results PSI-BLAST iteration3.png
• 11:53, 6 November 2025 Carol talk contribs created page File:GraphicSummary PB2.png
• 11:53, 6 November 2025 Carol talk contribs uploaded File:GraphicSummary PB2.png
• 11:19, 6 November 2025 Carol talk contribs created page File:Question2 answer.png
• 11:19, 6 November 2025 Carol talk contribs uploaded File:Question2 answer.png
• 10:28, 6 November 2025 Carol talk contribs created page Exercise PSI-BLAST ans (Created page with "NEW answers are being updated! == When BLAST fails == * '''QUESTION 1''': How many significant hits does BLAST find (E-value < 0.005)? Answer: No sequences with E-value below 0.005. ==Trying another approach== * '''QUESTION 2''': How many significant hits does BLAST find (E-value < 0.005)? Answer: After the first iteration, 494 hits are found. * '''QUESTION 3''': How large a fraction of the query sequence do the significant hits match (excluding the identical match)...")
• 17:49, 5 November 2025 Carol talk contribs created page File:PSI-BLAST firstrun.png
• 17:49, 5 November 2025 Carol talk contribs uploaded File:PSI-BLAST firstrun.png
• 14:17, 5 November 2025 Carol talk contribs created page Exercise PSI-BLAST (Created page with "Written by: Carolina Barra Quaglia ==Overview== In this exercise you will learn how to * Critically assess when BLAST fails (e.g., no significant hits) and explore alternative strategies. * Use PSI-BLAST to search for remote homologues of a given protein sequence (an orphan gene). * Interpret iterative PSI-BLAST output (number of hits, coverage, E-value, identity/positives) to assess significance. * Save and reuse a PSSM (profile) to search specialized databases (e.g.,...")
• 13:49, 5 November 2025 Carol talk contribs created page File:C22orf45.txt
• 13:49, 5 November 2025 Carol talk contribs uploaded File:C22orf45.txt
• 16:35, 27 October 2025 Carol talk contribs created page File:Epitopes Malaria exercise.png
• 16:35, 27 October 2025 Carol talk contribs uploaded File:Epitopes Malaria exercise.png
• 13:16, 27 October 2025 Carol talk contribs created page File:BepiPred2.png
• 13:16, 27 October 2025 Carol talk contribs uploaded File:BepiPred2.png
• 17:32, 9 October 2025 Carol talk contribs created page File:Question7c.png
• 17:32, 9 October 2025 Carol talk contribs uploaded File:Question7c.png
• 17:32, 9 October 2025 Carol talk contribs created page File:Question7b.png
• 17:32, 9 October 2025 Carol talk contribs uploaded File:Question7b.png
• 17:31, 9 October 2025 Carol talk contribs created page File:Question7a.png
• 17:31, 9 October 2025 Carol talk contribs uploaded File:Question7a.png
• 17:31, 9 October 2025 Carol talk contribs created page File:Question4c.png
• 17:31, 9 October 2025 Carol talk contribs uploaded File:Question4c.png
• 17:31, 9 October 2025 Carol talk contribs created page File:Question4b.png
• 17:31, 9 October 2025 Carol talk contribs uploaded File:Question4b.png
• 17:31, 9 October 2025 Carol talk contribs created page File:Question4a.png
• 17:31, 9 October 2025 Carol talk contribs uploaded File:Question4a.png
• 17:30, 9 October 2025 Carol talk contribs created page File:Question3.png
• 17:30, 9 October 2025 Carol talk contribs uploaded File:Question3.png
• 17:30, 9 October 2025 Carol talk contribs created page File:Question2.png
• 17:30, 9 October 2025 Carol talk contribs uploaded File:Question2.png
• 17:20, 9 October 2025 Carol talk contribs created page Protein Structure answers37 (Created page with "=Protein Structure - Answers= == '''Question 1.''' Look at the method X-RAY diffraction (Å). Which of the complexes is of better quality and why? == The PDB complex 7SBD, has the best resolution (lower Å). == Question 2. Provide a screenshot of the complex == <!-- == Q2 Are all hits are relevant if you are looking for a representative structure of the protein you entered? == No, some of the results (the last four) are not Rhamnogalacturonan acetylesterase at a...")
• 14:24, 7 October 2025 Carol talk contribs created page File:PyMOL tutorial.pdf
• 14:24, 7 October 2025 Carol talk contribs uploaded File:PyMOL tutorial.pdf
• 22:33, 6 October 2025 Carol talk contribs created page File:PyMOL show SEQ.png
• 22:33, 6 October 2025 Carol talk contribs uploaded File:PyMOL show SEQ.png
• 22:11, 6 October 2025 Carol talk contribs created page File:PyMOL panels.png
• 22:11, 6 October 2025 Carol talk contribs uploaded File:PyMOL panels.png
• 21:53, 6 October 2025 Carol talk contribs created page File:PDB.png