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converting to MAF or clustal format

Dear all,

Do you know any way to convert fasta or fatsq or tabulat to maf or clustal format. I want these formats for RNAcode. I checked already all the possibilities from Galexy and biopython but none of them worked. Many thanks in advance, Kind regards, Rahel

maf fasta fastq
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updated by Medhat Medhat • written by rahel14350 • rahel14350

Don't know for fastq but t_coffee provides a build in format reconversion utility. it can convert fasta_aln to clustal_aln. You can check this here

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written by microfuge microfuge

1 answer

There is in BioPython you can find it here

http://biopython.org/wiki/Multiple_Alignment_Format

with it you can read/write MAF file so in your case the input will be your alignment then you can write the output as MAF

also from fasta to clustal you can use

http://sequenceconversion.bugaco.com/converter/biology/sequences/fasta_to_clustal.php

or

from Bio.Align.Applications import ClustalwCommandline
ClustalwCommandline("clustalw", infile="your_file.fasta", outfile="output.aln")
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written by Medhat Medhat

Many thanks for your help, it works ...

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written by rahel14350 • rahel14350

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