PSI-BLAST (position specific iterative BLAST I think it stands for) and other BLAST variants may help - there are quite a few on NCBI now.
There are also some other nice tools such as HHPred at https://toolkit.tuebingen.mpg.de/. Maybe HMMer could be a good option too. I’m not sure if any of them would be fast though. Best wishes James On 16 Jan 2022, at 11:38, samer halabi <000030c2162795b2-dmarc-requ...@jiscmail.ac.uk> wrote: Dear All, Sorry to be disturbing you with my new inquiry. I always got great and trustworthy results using FUGUE (Protein homology recognition using environment-specific amino acid substitution tables: https://mizuguchilab.org/fugue/prfsearch.html<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmizuguchilab.org%2Ffugue%2Fprfsearch.html&data=04%7C01%7Ckriegerj%40PITT.EDU%7Cab9fce0d2e224081c05708d9d8e4a9fc%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637779299310177533%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=4cUXnoF8SZNqCF0GajGW1%2Fuzyc1AakxqF2PXH6f3QW0%3D&reserved=0>) I use an amino acid sequence of a viral protein of an unknown structure and function and with FUGUE it searches a structural database and gives very good results. When I use the protein BLAST for the same amino acid sequence, I may miss or get no results, especially when the identity is about 25% between the viral protein and the host protein it mimics . I tested that with a viral protein with known structure, and protein BLAST was not helpful. The only issue is that using FUGUE can be time consuming especially if I am searching for the possible function/structure of 100 viral proteins of one viral strain, not to mention that the same virus has several strains. What would be an efficient way to look for host protein mimics? I would greatly appreciate any suggestion. Thank you in advance. Best regards, Samer ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7Ckriegerj%40PITT.EDU%7Cab9fce0d2e224081c05708d9d8e4a9fc%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637779299310177533%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=r9Qyvc%2BHrdaGA6kBwP7J%2BfA%2F6vm%2FTOesr40IkAO5b%2Bw%3D&reserved=0> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
