<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>

CC BY-SA 4.0
2020-04-25T11:26:42.160Z
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.
M__
CC BY-SA 4.0
2020-04-25T11:29:08.763Z
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!
marilu
<blast><hidden-markov-models><hmmer>
phmm blast hmmer
# 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

