Extracting portion of fasta sequences from a multifasta file having contigs names and start-stop positions

[stefano_acquasanta]

Hello everyone! I am new to the community and also to galaxy. A collegue kindly explained to me how to download and how it works, but Id need a more specific consulence to know what tool should I use for my job. I am working with bacterial genomes, and I collected in a single file all the fasta sequences of the contigs composing the genomes of all the strains I am woorking with. I run a program for a phylogenetic analysis against all the contigs, looking for local alignment in each sequence with a reference cystein gene. As output I got a tab file with different columns, most important are the one with the names of the contigs and two with start and stop position of the alignment. Now the question: can I convert/creat a bed file that I could then use to extract the subsequences, which are the alignments, and this case which would be the best tool? Or in case the bed file is not suitable for prokariotic genes, what extension should I look for? I have so much to learn yet, so sorry if I may sound naive ahah thank you to whoever read up until here!