Hi Astrid When you do the blast between the assembled sequence and reference sequence both sequences need to be in single fasta format (i.e. not multiple fasta). The assembled sequence is likely to be in a multiple fasta format, so you will need to load that into Artemis first and save it out as a single fasta (from the menu: File->Write->All Bases->FASTA format). Then repeat the blast comparison using this and the coordinates for the blast hits will appear correctly in ACT along all scaffolds.
I am not sure why your scaffolds are ordered by size and how likely that is for your assembled sequence. Regards Tim On 1/5/12 9:36 AM, "Astrid von Mentzer" <[email protected]> wrote: > Hi, > > I have an assembled sequence (Velvet) which I have compared to a reference > sequence in ACT. I have run a blastall between the sequences. When I view the > comparison in ACT, the scaffolds are ordered in size with the biggest first > and only the biggest scaffold is compared to the reference sequence. > > What I wonder first is: Why are the scaffolds ordered according to size? How > do I make a comparison between all scaffolds (the whole sequence) to the > reference strain and not just one scaffold? > > I am new to this so please describe in detail so I understand. > > Cheers, > Astrid > > > _______________________________________________ > Artemis-users mailing list > [email protected] > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users _______________________________________________ Artemis-users mailing list [email protected] http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
