Multifasta files are not available for draft genomes in NCBI (or other places I've looked). How can I obtain such a file from a file holding contig/scaffold FASTA sequence? I do not need annotations. BLAST-based methods will be to time-consuming to use for many files so I guess a method would need to based on identifying orthologs by start and stop codons or use faster similarity-based methods such as RAPSearch?
i think cat contig*.fa > contigs.fa will be a better option if you have multiple files
hi all, I found that NCBI actually offers what I need after all. For every assembly, all separate contigs can be downloaded in a single file, and there is an option to select coding sequence only, which will result in a multifasta file. thanks a lot for your replies anyway! cheers Michiel
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