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i have created a phmm in hmmer from a multiple alignment focused on E. coli produced in tcoffee from sequences taken from blast similar to my query sequence.

  1. I would like to ask how i can compare the results from HMMER for a pHMM against UNIPROT (i used the phmm that i created and i searched in hmmer search against uniprot) and the results from BLAST.
  2. I would like to ask if i can search a pHMM in BLAST somehow, or if blast accepts only fasta one sequence.
  3. Why e-values of hmmer and blast are not comparable??Why e-value in hmmer is never 0? Thank you so much!!
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  • $\begingroup$ It would be useful to add the biological system you are working on. Multi-part questions don't really work, so the second part of your question is a separate question in my opinion. 1. Practicality of HMMER->UNIPROT. 2. Theories of e-values. Blast only accepts fasta, but conversion is easy, so programmatically its doable. $\endgroup$
    – M__ ♦
    Commented Apr 25, 2020 at 11:26
  • $\begingroup$ thanks!yes i should create a second post. it is about E.coli. and i am trying to compare the results taken from hmmer with the results taken from blast!thanks! $\endgroup$
    – marilu
    Commented Apr 25, 2020 at 11:29

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