Question: converting to MAF or clustal format
0
gravatar for rahel14350
3.7 years ago by
rahel1435030
United States
rahel1435030 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 • 1.7k views
ADD COMMENTlink modified 3.7 years ago by Medhat8.7k • written 3.7 years ago by rahel1435030

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 REPLYlink written 3.7 years ago by microfuge1.6k

Many thanks for your help

ADD REPLYlink written 3.7 years ago by rahel1435030
1
gravatar for Medhat
3.7 years ago by
Medhat8.7k
Texas
Medhat8.7k 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 COMMENTlink modified 3.7 years ago • written 3.7 years ago by Medhat8.7k

Many thanks for your help, it works ...

ADD REPLYlink written 3.7 years ago by rahel1435030
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