Multiple Sequence Alignment using HMM
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?
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