I have been using ACT with unfinished microbial sequence files
downloaded from TIGR. I have tried using these files ( each downloaded
file consisting of multiple individual sequence files of different
contigs) directly with the blastall command "formatdb" and then with
the blast program itself and the "-m 8" flag to output a comparison file
for ACT. This generates a useful line in the ACT display that shows the
contigs in different colours and the contig junctions, but the
comparison itself is incorrect. To get the correct comparison I have
been reformatting the downloaded TIGR file (which appears to be multiple
fasta format files anyway) as a single fasta file output from ARTEMIS
before using "formatdb" . Then the comparison file is good but I lose
the display of contig junctions. For my purposes I can keep two ACT
windows open, one showing the contig junctions and one the blast
comparisons. This works, but is there a better way to look at unfinished
sequence with ACT?
Tony Barbet
University of Florida
