Multiple Sequence Alignment using HMM

0

I have 3 fasta files of the human, mouse, and goat sequences and I want to align them by using Hidden Markov Model

I tried this :

 import Bio
    from Bio import SeqIO
    from Bio import Seq

    seq1 = SeqIO.read("Human.fasta","fasta")
    seq2 = SeqIO.read("Mouse.fasta","fasta")
    seq3= SeqIO.read("Goat.fasta","fasta")

    print(seq1)
from Bio import Align
aligner.mode="global"

score = aligner.score(seq1, seq2)
score

alignments = aligner.align(seq1, seq2)
for alignment in alignments:
    print(alignment)

But it is giving me the error:
ValueError: sequence has unexpected format

although the format is fasta I don't know why it is giving me this error

after that, I want to use HMM like :

from Bio.HMM import MarkovModel

a= MarkovModel.MarkovModelBuilder(seq1,seq2)
plt.plot(str(a))

But I am not getting the model which I required.

Can anyone help me to solve these 2 issues?


Bioinformatics


MSA


HMM

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