Hi Astrid You can load in the sequences from the command line:
act refH10407.fasta 6732_2#8_refH10407.crunch 6732_2#8_refH10407.fasta i.e. act subject_sequence comparison_file query_sequence Then (as per the documentation http://abacas.sourceforge.net/documentation.html) load in the tab file from the File menu. To compare another sequence against your reference you would need to use formatdb with the reference sequence, e.g. formatdb -p F -i refH10407.fasta Then using blastall: blastall -p blastn -m 8 -d refH10407.fasta -i other_sequence.fa -o comparison.blast Where other_sequence.fa¹ is the FASTA sequence of the other geneome. -m 8¹ generates the correct output format for ACT. Alternatively have a look at WebACT or Double ACT to generate the comparison for you: http://www.webact.org/WebACT/home http://www.hpa-bioinfotools.org.uk/pise/double_act.html Regards Tim On 2/23/12 9:06 AM, "Astrid von Mentzer" <[email protected]> wrote: > I have run ABACAS on my sequences and the following output files was the > result: > > 6732_2#8_refH10407.bin > 6732_2#8_refH10407.crunch > 6732_2#8_refH10407.fasta > 6732_2#8_refH10407.gaps > 6732_2#8_refH10407.gaps.stats > 6732_2#8_refH10407.gaps.tab > 6732_2#8_refH10407.tab > > I want to compare the sequence to my reference. > > In what place would I put which files? See below: > > ACT: > > Sequence 1: > Comparison file: > Sequence 2: > > I also want to view my sequence against another gene sequence. Correct me if I > am wrong, I would need to run a blast and then use the output comparison file > in ACT? Which blast script would one prefer? I have hear of blastall, blast by > MLST but I don't know why to choose either of them. > > Thanks in advance! > > Regards, > Astrid > --- > Astrid von Mentzer, PhD-student > University of Gothenburg > Institute of Biomedicine > Department of Microbiology and Immunology > Box 435 > 405 30 Göteborg > Sweden > > Phone: +46 31 786 62 21 > Fax: +46 31 786 62 05 > > > > > > > > _______________________________________________ > Artemis-users mailing list > [email protected] > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
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