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finding a protein on ENTREZ

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finding a protein on ENTREZ

Postby funkybioinformatics » Thu Mar 15, 2007 11:31 pm

ok, so i kno that protein 1 and protein 2 have the same function. I kno that protein 2 is in the ENTREZ database. Yet, a protein Blast agiasnt ENTREZ using protein 1 does not find protein 2 with a significant e.value. What gives? How can i re-define my search to find protein 2?
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Postby Dr.Stein » Fri Mar 16, 2007 2:14 am

Do you know the name or the structure or the characteristics of protein 2?
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Postby funkybioinformatics » Fri Mar 16, 2007 3:23 am

this is just a hypothetical question. no actualy proteins are involved here
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Postby mith » Fri Mar 16, 2007 3:39 am

change scoring? Functional similarities are not necessarily linked to sequence similarities.
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Postby blcr11 » Fri Mar 30, 2007 6:51 pm

That protein 1 and protein 2 have the same "function" doesn't neccessarily mean they have similar sequences. If you use too high a cut-off for similarity scores, or are too conservative with gap penalties and so on, Blast might not pick up a distant sequence homology. The simplest thing to do is to relax the constraints and search again.
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Postby blcr11 » Fri Mar 30, 2007 6:54 pm

...which is the same thing the moderator said, I see.
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Postby mith » Fri Mar 30, 2007 8:09 pm

:D , I like the validation
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Postby sarhi152 » Sat Apr 21, 2007 4:42 pm

If BLAST or any MSA cannot help, and if your proteins' structure are already solved, you can try SCOP (try google for the link 'cause I cannot post the URL until I have my 5th post :D )
SCOP classify proteins available in PDB on hierachical level - Protein with the same function but not so much similar in sequence can be found in the same superfamily.
You know the superfamily of protein 1, hopefully you find the protein 2 in this superfamily :)
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