User contributions for Carol

6 November 2025

• 10:5810:58, 6 November 2025 diff hist +22‎ Exercise PSI-BLAST ‎ →‎Trying another approach
• 10:2810:28, 6 November 2025 diff hist +10,080‎ N 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)..."

5 November 2025

• 19:5919:59, 5 November 2025 diff hist +19‎ Exercise PSI-BLAST ‎ →‎Finding a remote homolog (Optional)
• 19:5919:59, 5 November 2025 diff hist +88‎ Exercise PSI-BLAST ‎ →‎Reflection time
• 19:5619:56, 5 November 2025 diff hist −149‎ Exercise PSI-BLAST ‎No edit summary
• 19:3019:30, 5 November 2025 diff hist −561‎ Exercise PSI-BLAST ‎ →‎Trying another approach
• 19:2919:29, 5 November 2025 diff hist −289‎ Exercise PSI-BLAST ‎ →‎Saving and reusing the PSSM
• 19:0719:07, 5 November 2025 diff hist +145‎ Exercise PSI-BLAST ‎ →‎Saving and reusing the PSSM
• 19:0319:03, 5 November 2025 diff hist −145‎ Exercise PSI-BLAST ‎ →‎Saving and reusing the PSSM
• 19:0119:01, 5 November 2025 diff hist −96‎ Exercise PSI-BLAST ‎ →‎Saving and reusing the PSSM
• 18:5218:52, 5 November 2025 diff hist +220‎ Exercise PSI-BLAST ‎ →‎Saving and reusing the PSSM
• 18:4718:47, 5 November 2025 diff hist +239‎ Exercise PSI-BLAST ‎ →‎Saving and reusing the PSSM
• 18:3718:37, 5 November 2025 diff hist +508‎ Exercise PSI-BLAST ‎ →‎Saving and reusing the PSSM
• 18:2818:28, 5 November 2025 diff hist +12‎ Exercise PSI-BLAST ‎ →‎Constructing the PSSM
• 18:2718:27, 5 November 2025 diff hist −92‎ Exercise PSI-BLAST ‎ →‎Constructing the PSSM
• 18:2618:26, 5 November 2025 diff hist +137‎ Exercise PSI-BLAST ‎ →‎Constructing the PSSM
• 18:0018:00, 5 November 2025 diff hist +271‎ Exercise PSI-BLAST ‎ →‎Trying another approach
• 17:5817:58, 5 November 2025 diff hist 0‎ Exercise PSI-BLAST ‎ →‎Constructing the PSSM
• 17:5317:53, 5 November 2025 diff hist +6‎ Exercise PSI-BLAST ‎ →‎Constructing the PSSM Tag: Manual revert
• 17:5317:53, 5 November 2025 diff hist +1‎ Exercise PSI-BLAST ‎ →‎Constructing the PSSM
• 17:5317:53, 5 November 2025 diff hist −6‎ Exercise PSI-BLAST ‎ →‎Constructing the PSSM
• 17:5317:53, 5 November 2025 diff hist −1‎ Exercise PSI-BLAST ‎ →‎Constructing the PSSM
• 17:5217:52, 5 November 2025 diff hist 0‎ Exercise PSI-BLAST ‎ →‎Constructing the PSSM
• 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.,..."