User contributions for Carol

5 November 2025

• 17:5217:52, 5 November 2025 diff hist +138‎ Exercise PSI-BLAST ‎ →‎Trying another approach
• 17:5017:50, 5 November 2025 diff hist +6‎ Exercise PSI-BLAST ‎ →‎Constructing the PSSM
• 17:5017:50, 5 November 2025 diff hist +54‎ Exercise PSI-BLAST ‎ →‎Constructing the PSSM
• 17:4917:49, 5 November 2025 diff hist 0‎ N File:PSI-BLAST firstrun.png ‎No edit summary current
• 17:4717:47, 5 November 2025 diff hist +1‎ Exercise PSI-BLAST ‎ →‎Trying another approach
• 17:3317:33, 5 November 2025 diff hist +271‎ Exercise PSI-BLAST ‎ →‎Trying another approach
• 17:2717:27, 5 November 2025 diff hist −340‎ Exercise PSI-BLAST ‎ →‎Trying another approach
• 14:5514:55, 5 November 2025 diff hist −12‎ Exercise PSI-BLAST ‎ →‎Trying another approach
• 14:4114:41, 5 November 2025 diff hist +10‎ Exercise PSI-BLAST ‎ →‎When BLAST fails
• 14:4114:41, 5 November 2025 diff hist +110‎ Exercise PSI-BLAST ‎ →‎When BLAST fails
• 14:3814:38, 5 November 2025 diff hist +150‎ Exercise PSI-BLAST ‎ →‎When BLAST fails
• 14:3414:34, 5 November 2025 diff hist −239‎ Exercise PSI-BLAST ‎ →‎When BLAST fails
• 14:3214:32, 5 November 2025 diff hist −48‎ Exercise PSI-BLAST ‎ →‎When BLAST fails
• 14:2914:29, 5 November 2025 diff hist +4‎ Exercise PSI-BLAST ‎ →‎When BLAST fails
• 14:2814:28, 5 November 2025 diff hist −2‎ Exercise PSI-BLAST ‎ →‎When BLAST fails
• 14:2814:28, 5 November 2025 diff hist +47‎ Exercise PSI-BLAST ‎ →‎When BLAST fails
• 14:2714:27, 5 November 2025 diff hist +3‎ Exercise PSI-BLAST ‎ →‎When BLAST fails
• 14:2514:25, 5 November 2025 diff hist −5‎ Exercise PSI-BLAST ‎ →‎When BLAST fails
• 14:2514:25, 5 November 2025 diff hist −4‎ Exercise PSI-BLAST ‎ →‎When BLAST fails
• 14:2414:24, 5 November 2025 diff hist +1‎ Exercise PSI-BLAST ‎ →‎When BLAST fails
• 14:2414:24, 5 November 2025 diff hist 0‎ Exercise PSI-BLAST ‎ →‎When BLAST fails
• 14:2314:23, 5 November 2025 diff hist +2‎ Exercise PSI-BLAST ‎ →‎When BLAST fails
• 14:2214:22, 5 November 2025 diff hist +9‎ Exercise PSI-BLAST ‎No edit summary
• 14:2114:21, 5 November 2025 diff hist −4‎ Exercise PSI-BLAST ‎ →‎When BLAST fails
• 14:2114:21, 5 November 2025 diff hist +172‎ Exercise PSI-BLAST ‎ →‎When BLAST fails
• 14:1714:17, 5 November 2025 diff hist −246‎ Exercise PSI-BLAST ‎ →‎Introduction: What are orphan genes?
• 14:1714:17, 5 November 2025 diff hist +14,551‎ N 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.,..."
• 13:4913:49, 5 November 2025 diff hist 0‎ N File:C22orf45.txt ‎No edit summary current
• 12:0812:08, 5 November 2025 diff hist +1‎ ExPSIBLAST ‎ →‎Trying another approach
• 12:0812:08, 5 November 2025 diff hist −387‎ ExPSIBLAST ‎ →‎Trying another approach
• 11:5911:59, 5 November 2025 diff hist 0‎ ExPSIBLAST ‎ →‎Trying another approach
• 11:5811:58, 5 November 2025 diff hist 0‎ ExPSIBLAST ‎ →‎Trying another approach
• 11:5711:57, 5 November 2025 diff hist +289‎ ExPSIBLAST ‎ →‎Trying another approach
• 11:5011:50, 5 November 2025 diff hist +21‎ ExPSIBLAST ‎ →‎When BLAST fails
• 11:4811:48, 5 November 2025 diff hist +21‎ ExPSIBLAST ‎ →‎When BLAST fails
• 10:3110:31, 5 November 2025 diff hist +1‎ ExPSIBLAST ‎ →‎When BLAST fails
• 10:3010:30, 5 November 2025 diff hist +1‎ ExPSIBLAST ‎ →‎When BLAST fails
• 10:3010:30, 5 November 2025 diff hist +5‎ ExPSIBLAST ‎ →‎When BLAST fails

3 November 2025

• 18:5718:57, 3 November 2025 diff hist +24‎ Exercise: Construction of sequence logos and weight matrices ‎ →‎Background: Peptide MHC binding
• 18:5618:56, 3 November 2025 diff hist +1‎ Exercise: Construction of sequence logos and weight matrices ‎ →‎Background: Peptide MHC binding
• 18:5518:55, 3 November 2025 diff hist −40‎ Exercise: Construction of sequence logos and weight matrices ‎ →‎Small training set
• 18:5218:52, 3 November 2025 diff hist +44‎ Exercise: Construction of sequence logos and weight matrices ‎ →‎Identification of MHC binding motifs
• 18:5118:51, 3 November 2025 diff hist −252‎ Exercise: Construction of sequence logos and weight matrices ‎ →‎Identification of MHC binding motifs

30 October 2025

• 14:0414:04, 30 October 2025 diff hist +10‎ Exercise: The protein database UniProt ‎ →‎The contents of UniProt

28 October 2025

• 17:2817:28, 28 October 2025 diff hist −7‎ Exercise:Malaria Vaccine ‎ →‎Searching UniProt current
• 17:2417:24, 28 October 2025 diff hist +8‎ Exercise:Malaria Vaccine ‎ →‎Searching UniProt
• 14:1814:18, 28 October 2025 diff hist +65‎ Exercise:Malaria Vaccine ‎ →‎Epitope prediction
• 14:1214:12, 28 October 2025 diff hist 0‎ Exercise:Malaria Vaccine ‎ →‎Prediction of B-cell epitopes in a membrane protein

27 October 2025

• 16:3516:35, 27 October 2025 diff hist −1‎ Answers:Malaria Vaccine ‎ →‎5 - Visualization of epitopes current
• 16:3516:35, 27 October 2025 diff hist 0‎ N File:Epitopes Malaria exercise.png ‎No edit summary current