Tõnu,
the problem is that blastall is doing searches on all of the sequences within the fasta database files, but is reporting match coordinates individually for each sequence. ACT will read all of the coordinates as if they were from a single sequence comparison.
The way to resolve this is to read each fasta database file into Artemis, and write each out again as a single sequence "Write/all bases/fasta format"
Then do the blastall of one single sequence against the other.
Finally, launch ACT with each of the original multiple fasta database files, but with the comarison file generated above.
yours,
Julian Parkhill.
Tõnu Margus wrote:
Hi,
I am first time artemis user and asking my be trivial things but I didnt found answers from mailing list archive.
So,
I am using artemis ver6 on LINUX and had poblems with
correct positioning of the blast search results by artemis according to the entry sequence.
I run blast against entri sequence ( blastall -p blastn -m8 -e 1e-10 -i my_input.fa -d my_blastdb > my_input.blastn )
The result file is recognized but artemis shows that match is started from the beginning of query sequence what is not true.
It did not help if I use MPScrunch ( wiht options -x ot -d) for converting blast output in to another format.
Is it normal behaivor of artemis or I missed something important?
From examples I see that blast output (example.blastn.tab) is converted in to EMBL feature format.
Is it the solution? I didnt found converters jet.
Thanks
Tõnu Margus
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-- Julian Parkhill Senior Investigator, 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/Microbes http://www.sanger.ac.uk/Teams/faculty/parkhill
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