Fasta To Maf Converter

Question

[Rahul]

I want to study a lot of fasta sequences . I want to do a comparative study by reshuffling among the sequences. I want to use MultiZ which accepts MAF file format as input. Please suggest me the if tool available of suggest me the scripts preferably in perl.

Thanks

[Eric Fournier]

If you have plain old fasta sequences, see Hamish's comment. If you have FASTA -alignments- and you absolutely want to convert those directly to MAF, there is a branch of biopython which has a MAF reader/writer. Thus you could use Bio.AlignIO to read in your FASTA alignment then write it back out in the MAF format.

[Joseph Hughes]

Can you please specify whether it is the Multiple Alignment Format or the Mutation Annotation Format that you are interested in.

[Rahul]

Sir, Here MAF is Multiple Alignment Format. I want to study Blocks conserved using Threaded Block Aligner(TBA). Please Help.

Thanks

[Hamish]

From the MultiZ and TBA documentation (see http://www.bx.psu.edu/miller_lab/) the usual usage of TBA starts with a step that uses BLASTZ to generate lav files which are converted into a MAF files to use as input to 'tba'. What is the reason that you want to skip this step?

Answer 1

[Bio_Kas]

Hello Guys, Is there a tool to convert fasta file of multiple alignments into a maf-format file.

[Eric Fournier]

See my comment to the original question. Also, please do not post question as answers. If you want to ask a new question, do so using the "Ask question" button.

Answer 2

[irinagaranina24]

it is impossible convert fasta to maf. Maf-format alignment have more data than fasta.It's like convert fasta to fastq.