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Question: converting to MAF or clustal format
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gravatar for rahel14350
4.3 years ago by
rahel14350 • 30
United States
rahel14350 • 30 wrote:

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
fastq fasta maf • 2.0k views
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modified 4.3 years ago by Medhat ♦ 8.8k • written 4.3 years ago by rahel14350 • 30

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

ADD REPLY • link written 4.3 years ago by microfuge • 1.9k

Many thanks for your help

ADD REPLY • link written 4.3 years ago by rahel14350 • 30
1
gravatar for Medhat
4.3 years ago by
Medhat ♦ 8.8k
Texas
Medhat ♦ 8.8k wrote:

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")
ADD COMMENT • link modified 4.3 years ago • written 4.3 years ago by Medhat ♦ 8.8k

Many thanks for your help, it works ...

ADD REPLY • link written 4.3 years ago by rahel14350 • 30
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