April 25, 2005 - Using FASTA-format Files
Question:
My fasta-format sequence file contains more than one sequence. Do I have to edit it by hand to create individual sequence files?
Answer:
The GCG program FromFasta can extract the sequences from a multiple-sequence fasta-format file and create individual GCG-format sequence files. If you use the -listfile command-line parameter, it also creates a list file containing the names of each of the newly created sequences. You can use this list file as input to programs that can accept multiple sequences.
% fromfasta all_orfs.fa -listfile=all_orfs.list
This creates one GCG-format sequence file for each sequence in the fasta-format file all_orfs.fa and a list file named all_orfs.list that contains the names of each of the new sequence files. To create a multiple sequence alignment of all of these sequences with PileUp:
% pileup @all_orfs.list
