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Could this Pham be improperly assigned in PECAAN?
| Link to this post | posted 25 Mar, 2020 23:49 | |
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Why isn’t there a Pham report for a Pham that seems very common in the databases? Here is an example: Magic8 gene 92 Nothing behind the pham link - no PDF - I think that means it’s not on http://phages.wustl.edu/starterator/ . Yet, many BLAST hits for this gene/protein! Wouldn't a frequently found protein be assigned a Pham and have a starterator analysis done? Thanks. John |
| Link to this post | posted 26 Mar, 2020 18:30 | |
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missing or broken links are almost always due to pham changes with each new database release. New databases typically come out at least once a week. Once a database has been released by the Hatfull lab it takes each subsystem a variable amount of time to update. phagesdb.org will update almost immediately since it is also in the Hatfull lab. Phamerator.org and Pecaan will typically update pretty quickly as all they need to do is download and install the new database. Starterator will almost always update last as it takes quite a bit of time to run 15,000 clustal alignments and create the 15,000 reports. Phamerator.org, pecaan and starterator all have a way to see which database version they are on: phagesdb see: http://phamerator.webfactional.com/databases_Hatfull/Actino_Draft.version starterator see: http://phages.wustl.edu/starterator/database.version pecaan: look on any "pham maps" page just above the map phamerator.org: open the pull down menu in the top left |