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- 09:28, 6 November 2025 Exercise PSI-BLAST ans (hist | edit) [8,083 bytes] Carol (talk | contribs) (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)...")
- 13:17, 5 November 2025 Exercise PSI-BLAST (hist | edit) [16,068 bytes] Carol (talk | contribs) (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.,...")
- 16:20, 9 October 2025 Protein Structure answers37 (hist | edit) [5,130 bytes] Carol (talk | contribs) (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...")
- 18:33, 6 October 2025 Protein Structure (hist | edit) [9,156 bytes] Carol (talk | contribs) (Created page with "''By Carolina Barra Quaglia'' == Overview == In this exercise you will learn how to * Search diferent protein databases to obtain protein structures. * Critically choose the best structure, when more than one is available. * Visualize a protein structure using PyMOL * Highlight features of interest and perform a basic alignment. This exercise is written a bit different. Instead of the step wise exercise we are going to try a different method called inquiry-based learni...")