Bala,
ACT cannot reconstruct the positional information for the separate
sequences within a multiple FASTA file; BLAST reports only the local
coordinates for the matches. What you need to do is:
1) Concatenate all the mFASTA sequences into a single sequence for
each genome (you can do this from Artemis, using the "Write; all
bases" menu)
2) Do the blast comparison with the concatenated sequences
3) Load the original multiple FASTA files into ACT, but use the
comparison file from the concatenated sequences. You should see the
contigs represented by alternating dark/light brown features, plus
the matches for the whole sequences.
For the other problem; the set cutoffs only remain for as long as the
dialog window is open. Closing the dialog window resets the cutoffs.
yours,
Julian.
On 6 Nov 2006, at 16:50, [EMAIL PROTECTED] wrote:
Dear Julian
I am comparing them using multiple fasta sequences within a single
file
that represent one contig, such as a chromosome or plasmid.
Do I need to do single contig sequences? I did not think so.
Regards
BALA.
On Mon, 6 Nov 2006, Julian Parkhill wrote:
Dr. Ganesan,
are these genomes represented as single sequences, or are they
multiple FASTA files?
yours,
Julian.
On 5 Nov 2006, at 08:23, BALASUBRAMANIAN GANESAN wrote:
Hello
I am using ACT v5 for the Mac to look at a two-genome comparison to
start off
with.
Many features seem to not work such as score cutoff, percent ID
cutoff are
never apllied or saved after
setting them. The sequence lock works totally at random.
But my main problem is that the comparison view shows only the
comparisons for
the first 5-6k bases for
2.5 Mb genomes. Why is this the case?
I am running OSX-10.4.3 and using blastall text o/p directly as the
comparison
file generated by the
blastn option using -m 8 to generate a tabular output. I had the
display
problem after trying the unix
version of ACT on my Mac also. I recreated my blast comparison
without a
specified e-value and still had
the problem.
What can possibly cause this issue?
Kindly help.
Thank you,
Regards,
Dr. BALASUBRAMANIAN GANESAN
Research Group Leader - BioSystems Modelling
Service Group Leader - Bioinformatics
CENTER FOR INTEGRATED BIOSYSTEMS
UMC-4700
UTAH STATE UNIVERSITY
LOGAN UT-84322.
US OF A.
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Julian Parkhill
Head of the Pathogen Sequencing Unit,
The Sanger Institute,
Wellcome Trust Genome Campus,
Hinxton, Cambridge, CB10 1SA, UK
Visiting Professor in Microbial Genomics,
University of Oxford
Tel: +44(0)1223 494975, Fax: +44(0)1223 494919
http://www.sanger.ac.uk/Projects/Pathogens
http://www.sanger.ac.uk/Teams/faculty/parkhill
Julian Parkhill
Head of the Pathogen Sequencing Unit,
The Sanger Institute,
Wellcome Trust Genome Campus,
Hinxton, Cambridge, CB10 1SA, UK
Visiting Professor in Microbial Genomics,
University of Oxford
Tel: +44(0)1223 494975, Fax: +44(0)1223 494919
http://www.sanger.ac.uk/Projects/Pathogens
http://www.sanger.ac.uk/Teams/faculty/parkhill
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