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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).
- 15:43, 21 September 2026 Carol talk contribs created page ExBlast-Answers new (Created page with "Answers to the BLAST exercise. Values for database sizes etc. retrieved September 21, 2026 ==Part 1: Your first BLAST search== ===QUESTION 1.2=== * ''what is the identifier (Accession)?'' :OL351605 or M57671 (Note that the latter was also part of the sequence name for your query sequence!) * ''what is the alignment score ("Max score in bits")?'' :The max score is 780 bits (Raw score is 864) * ''what is the percent identity and query coverage?'' :100% * ''what is the E...")
- 15:37, 21 September 2026 Carol talk contribs created page File:BLAST Saved Strategies.png
- 15:37, 21 September 2026 Carol talk contribs uploaded File:BLAST Saved Strategies.png
- 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...")
- 17:38, 3 September 2026 Henni talk contribs created page File:PDB9R4E.png
- 17:38, 3 September 2026 Henni talk contribs uploaded File:PDB9R4E.png
- 12:03, 28 August 2026 Raz talk contribs created page File:Taxonomy AI answer 2026 extC.jpg
- 12:03, 28 August 2026 Raz talk contribs uploaded File:Taxonomy AI answer 2026 extC.jpg
- 12:02, 28 August 2026 Raz talk contribs created page File:Taxonomy AI answer 2026 extB.jpg
- 12:02, 28 August 2026 Raz talk contribs uploaded File:Taxonomy AI answer 2026 extB.jpg
- 12:01, 28 August 2026 Raz talk contribs created page File:Taxonomy AI answer 2026 extA.jpg
- 12:01, 28 August 2026 Raz talk contribs uploaded File:Taxonomy AI answer 2026 extA.jpg
- 11:39, 28 August 2026 Raz talk contribs created page File:Taxonomy AI answer 2026.jpg
- 11:39, 28 August 2026 Raz talk contribs uploaded File:Taxonomy AI answer 2026.jpg
- 11:16, 28 August 2026 Raz talk contribs created page Using the Taxonomy database ANSWERS (Initial copy over of the old answer set)
- 20:53, 27 August 2026 Raz talk contribs created page File:NcbiCommonTree2026.jpg
- 20:53, 27 August 2026 Raz talk contribs uploaded File:NcbiCommonTree2026.jpg
- 20:05, 27 August 2026 Raz talk contribs created page File:NcbiTax2026.jpg
- 20:05, 27 August 2026 Raz talk contribs uploaded File:NcbiTax2026.jpg
- 19:37, 27 August 2026 Raz talk contribs created page Using the Taxonomy database (Initial copy over of the old exercise)
- 16:45, 3 August 2026 Henni talk contribs created page 22111:Course plan autumn 2026 (Created page with "== General information == === Where and when === Lectures plus subsequent exercises will take place every Tuesday afternoon during the semester, starting '''Tuesday Sep 2 at 13:00'''. Lectures will be from 13:00 to approx. 14 in '''Aud. 54, building 208''', and the exercises will then take place in '''the group rooms ALC1 (001), ALC2 (011), ALC4 (012), and "Touch Down" (024) also in building 208'''. === Teachers === * [http://www.dtu.dk/service/telefonbog/person?id=...")
- 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...")
- 23:00, 26 November 2025 Henni talk contribs created page File:Ribosomal proteins 35-NJ tree.rerooted+annotated.png
- 23:00, 26 November 2025 Henni talk contribs uploaded File:Ribosomal proteins 35-NJ tree.rerooted+annotated.png
- 22:57, 26 November 2025 Henni talk contribs created page File:Ribosomal proteins 35-NJ tree.rerooted.png
- 22:57, 26 November 2025 Henni talk contribs uploaded File:Ribosomal proteins 35-NJ tree.rerooted.png
- 22:44, 26 November 2025 Henni talk contribs created page File:Ribosomal proteins 35-NJ tree.unrooted.newick.txt
- 22:44, 26 November 2025 Henni talk contribs uploaded File:Ribosomal proteins 35-NJ tree.unrooted.newick.txt
- 22:43, 26 November 2025 Henni talk contribs created page File:Ribosomal proteins 35-NJ tree.unrooted.png
- 22:43, 26 November 2025 Henni talk contribs uploaded File:Ribosomal proteins 35-NJ tree.unrooted.png
- 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
