Body: <p>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.</p>
  <ol>
  <li>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.</li>
  <li>I would like to ask if i can search a pHMM in BLAST somehow, or if blast accepts only fasta one sequence.</li>
  <li>Why e-values of hmmer and blast are not comparable??Why e-value in hmmer is never 0?
  Thank you so much!!</li>
  </ol>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-25T11:26:42.160Z
Comments.Text: 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.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-25T11:29:08.763Z
Comments.Text: 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!
Comments.UserDisplayName: marilu
Tags: <blast><hidden-markov-models><hmmer>
Title: phmm blast hmmer
ThreadText: # phmm blast hmmer
  
  (Asked by: username_0 on 2020-04-25)
  
  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!!
  
  **Tags:** blast, hidden-markov-models, hmmer
  
  > **Comments:**
  > **username_1**: 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.  
  > **username_0**: 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!  
  
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  ## 0 answers
  
  