In message <[EMAIL PROTECTED]> you wrote:
>If you use the "-d" flag for MSPcrunch output, then Artemis will read
>the resulting file directly.
Thanks. I also received some information from elsewhere suggesting that
artemis can read blast reports that are generated with the -m8 flag:
-----------------------------------------------
The development version of ACT now supports two new input file
formats, which may make things easier for you:
* BLAST version 2.2.2 output: The blastall command must run with
the -m 8 flag which generates one line of information per
HSP. Artemis can read this output too.
* MEGABLAST output: ACT can also read the output of MEGABLAST,
which is part of the NCBI blast distribution.
I recommend using NCBI BLAST version 2.2.2 and the -m 8. This
combination works well for comparing sequences up to the size of small
genomes. Megablast is much faster for large sequences, but is less
sensitive.
-----------------------------------------------
Is there any particular "trick" to getting artemis to read this -m8 output?
Trying to read the file or read it is as a feature produces a horrible java
error (I'll spare this list the full details), so presumably I am using the
wrong technique.
Thanks,
Milo.
--
Milo Thurston, CEH Oxford, Mansfield Road, Oxford, OX1 3SR.
'phone 01865 281658, fax 01865 281696.
http://www.bioinf.ceh.ac.uk/lab/
