Dear Anna,
thanks a lot for sending me a mauve version (mauve_temp) that can load feature
annotation.
Is in mean time a stable version that includes the load feature annotation
available?
Up to now I got no response from you about my problem I send to you in june,
here it is again.
After moving contigs I still have a problems with the type, that is always asap
contig label strand left_end right_end prev_left
prev_right reversed type
AAUP02000001 A35_A1136 complement 97352 99368 97352 99368
false asap
AAUP02000001 A35_A1092 forward 63369 63869 63369 63869 false
asap
AAUP02000001 GI:120576473 forward 10563 11564 10563 11564 false
asap
AAUP02000001 GI:120576479 forward 2064 2837 2064 2837 false
asap
AAUP02000001 GI:120576465 forward 11566 12234 11566 12234 false
asap
AAUP02000001 rnr complement 56374 58584 56374 58584 false
asap
May be do to a problem in ChangedFeatureWriter.java
case TYPE_IND:
return "asap";
Also it would be nice if I could add an additional type like repeat.
Would it be possible to color it in the application like it is done for
tRNA=green or rRNA=red?
Additional it would be fine to load also the description of the gene, how I
could do this?
If you or someone from the mauve team have a solution it would be great.
Thanks in advance for your help,
best regards
Martin
--
Dr. Martin Münsterkötter
MIPS - Institute of Bioinformatics and Systems Biology
Helmholtz Zentrum München
German Research Center for Environmental Health (GmbH)
Ingolstädter Landstr. 1
85764 Neuherberg
Germany
http://www.helmholtz-muenchen.de/mips
Phone: +49-89-3187-3579
Fax: +49-89-3187-3585
Chairman of Supervisory Board: MinDir Dr. Peter Lange
Board of Directors: Prof. Dr. Günther Wess and Dr. Nikolaus Blum
Register of Societies: Amtsgericht München HRB 6466
________________________________________
Von: Münsterkötter, Martin, Dr.
Gesendet: Dienstag, 1. Juni 2010 17:27
An: ANNA INDIGO RISSMAN
Cc: Münsterkötter, Martin, Dr.
Betreff: AW: Mauve - reordered annotations
Dear Anna,
thanks a lot for sending me a mauve version (mauve_temp) that can load feature
annotation.
After moving contigs I still have a problems with the type, that is always asap
contig label strand left_end right_end prev_left
prev_right reversed type
AAUP02000001 A35_A1136 complement 97352 99368 97352 99368
false asap
AAUP02000001 A35_A1092 forward 63369 63869 63369 63869 false
asap
AAUP02000001 GI:120576473 forward 10563 11564 10563 11564 false
asap
AAUP02000001 GI:120576479 forward 2064 2837 2064 2837 false
asap
AAUP02000001 GI:120576465 forward 11566 12234 11566 12234 false
asap
AAUP02000001 rnr complement 56374 58584 56374 58584 false
asap
May be do to a problem in ChangedFeatureWriter.java
case TYPE_IND:
return "asap";
Also it would be nice if I could add an additional type like repeat.
Would it be possible to color it in the application like it is done for
tRNA=green or rRNA=red?
Thanks in advane for your help,
best regards
Martin
--
Dr. Martin Münsterkötter
MIPS - Institute of Bioinformatics and Systems Biology
Helmholtz Zentrum München
German Research Center for Environmental Health (GmbH)
Ingolstädter Landstr. 1
85764 Neuherberg
Germany
http://www.helmholtz-muenchen.de/mips
Phone: +49-89-3187-3579
Fax: +49-89-3187-3585
Chairman of Supervisory Board: MinDir Dr. Peter Lange
Board of Directors: Prof. Dr. Günther Wess and Dr. Nikolaus Blum
Register of Societies: Amtsgericht München HRB 6466
________________________________________
Von: ANNA INDIGO RISSMAN [[email protected]]
Gesendet: Mittwoch, 28. April 2010 18:18
An: Münsterkötter, Martin, Dr.
Betreff: Mauve - reordered annotations
Hi. Sorry for the delay in response, it took your email a little while to
reach me, and a little longer to figure out the best solution.
Yes, currently there is no feature for reloading reordered annotation. It
should be present in an upcoming, and in the meantime, I can send you a version
with a beta feature enabled.
To use the code I'm sending, copy the file into your Mauve install directory
(Mauve 2.3.1, probably in program files). Then, instead of clicking the
shortcut to run Mauve, double-click the file you just placed in the directory.
(Let me know if you have trouble with any of this). It should run exactly as
normal, but have an additional menu option under "File" called "Import
Annotations". Select your draft genome from the drop-down, and load the
your_genome_features.tab file using the filechooser. That should load them. . .
Let me know if you're still having trouble
Anna Rissman
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