When doing comparative genomics analysis, we need to order the assembled contigs against a reference genome using Mauve or MUMmer.

In the case of using Mauve, we need to prepare a comparison file, or a crunch file. To generate the file, one can upload the genome sequences in genbank/embl/fasta format to WebACT, or upload sequences in fasta format to Double ACT (It has been reported that genbank format didn’t work well with DoubleACT1), then wait for their notification when finished.

Alternately, one can generate a crunch file locally using blastall like this:

if [ $# -ne 4 ]; then 
    echo -e "\nUsage: $0 [blastn/tblastx] [input_first_genome.fna] [input_second_genome.fna] [output_filename]\n"
    exit 1

# run formatdb
formatdb -p F -i $2 

# do blastall with 30 cores
blastall -p $1 -m 8 -e 1e-5 -d $2 -i $3 -o $4 -a 30

Besides, ACT works just like Artemis, except gbk file, a gff file can be loaded as well for annotations.

To sum up, here is the steps need to be done:

  1. get genome sequences in fasta format
  2. do pairwise blastn search to generate the comparison crunch files.
  3. load the genome fasta and crunch files
  4. load the annotation files in gff format
  1. https://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00372.html