Question: How to remove bases out of codon frame
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gravatar for kaz0816
11 days ago by
kaz08160
kaz08160 wrote:

Please tell me how to efficiently remove bases that are out of the codon frame as follows. Protein: [N-ter]- S D C V E I L T N C A -[C-ter]

Nucleotide: [5']- G TCA GAC TGC GTA GAA ATT CTT ACA AAT TGT GCA GA -[3']

I aligned the nucleotide sequences based on the amino acid alignment with the backtrans option of Trimal. However, the extra bases cause misalignment of nucleotide sequences, so I am looking for ways to remove the out-of-frame bases.

Best regards,

sequence alignment • 72 views
ADD COMMENTlink modified 11 days ago • written 11 days ago by kaz08160

How is the data presented in its raw form? Add some more detail about the input and expected output.

ADD REPLYlink written 11 days ago by rpolicastro720

Raw data are nucleotide sequences and amino acid sequences from 4 species in FASTA format. Nucleotide sequences do not necessarily start with an open reading frame, but with one or two extra bases. On the other hand, the amino acid sequences does not start with a "X" to correspond to the extra bases.

I arranged the nucleotide sequences so that they correspond to amino acids according to the following flow, but the work does not complete normally due to the extra bases.

$ mafft-linsi amino_acid.fasta > amino_acid.aln

$ trimal -automated1 -ignorestopcodon -in amino_acid.aln -backtrans nucleotide.fasta -out output1.fasta

$ trimal -nogaps -in output1.fasta -out output2.fasta

ADD REPLYlink modified 11 days ago • written 11 days ago by kaz08160
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