Hi Everyone, I'm working with MAUVE. I'm interested in certain regions that are present in one of my genomes, but no on the others in the alignment. What I did is that I used the backbone file, and pick the regions that have coordinates for that genome (cero I assumed was absent of the region). Additionally, I made a script to use the coordinates in the backbone file to extract from the genome the sequences of interest. I have several assumptions about the way the coordinates on the backbone file reflect the information in the genomes. However, I have been getting weird sequences, this lead me to ask you several questions, hoping you could help me.
1. When I have a fragmented genome, I have a multi-fasta file representing this genome. When I want to extract the sequences using the coordinates from the backbone file, what assumptions do I have to make to deal with the different contigs. How does Mauve make the counting over a multifasta file?. Is Mauve counting the letters in the headers? Do the coordinates re-start each time that a header appears, I mean, for each contig in my fasta file, Mauve starts from 1 again? 2. How do I deal with the negative coordinates? Do I extract the sequences, an then make the reverse of that sequence? or Do I extract those coordinates of the whole genome reversed? Do I have to start counting from the end of the sequence, to the begining? 3. Is there available an utility that helps me with these issues? Thanks very much for your attention! -- Laura Perlaza-Jiménez Graduate Research Assistant Mycology and Plant Pathology Laboratory (LAMFU) Universidad de Los Andes. Bogotá, Colombia.
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