Hi Sun-young
You can load your own plots into Artemis/ACT. If you look at the section
in the manual on the Graph Menu and the sub-section 'Add User Plot...'.
This describes the available formats you will need the data to be in. ACT
has menus for each of the sequences you load in and you will need to
format the user plot so that it is against one of the sequences.
However have you just tried zooming out (with the scroll bars on the
right of the feature displays) to get the overview of reverse matches? The
reverse matches are in blue. You can select them by clicking on them and
from the File menu Write the bases of selection.
Regards
Tim
On Sun, 11 Jul 2010, sylee wrote:
Dear Tim.
Hi, Thank you for your answer
and.. I have more questions..
I want to see where reversed matches are and get sequences of there.
in main window(loading 2 sequences files, comparison file), I have to move the
scroll bar and find where reverse/forward matches are.
but if I load a dot-plot file, I can see at a glance, i think.. so I am
trying to load the dot plot file.
following ACT manual, ACT can read users dot-plot. also, I have a plot file
generated MUMmer.
when I upload 2 fasta files and comparison file, the menu bars are changed.
they have functions for each fasta file I loaded.
I have one dot plot file compared two sequence,.
1. where I upload this file?
2. if I upload a dot-plot file generated mummerplot, do I need a parser?
(following manual, mummmerplot output is different from users plot format
recommended ACT, so I got error message when I upload)
3. if I upload a dot-plot file, can I select a region and get sequences of
there?
best regards.
Sun-young
2010. 6. 28., 오후 4:50, Tim Carver 작성:
Hi
There are some useful examples on how to parse the output here:
http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00487.html
You can get the selected sequence either by going to the View menu and
clicking the 'Bases of Selection as FASTA', or from the File menu under the
'Write' option you can write out the bases of selection.
Regards
Tim
On 6/27/10 10:10 AM, "sylee" <209ab...@gmail.com> wrote:
Dear Sir/Ma'am
Hi, I am trying to view the comparison files using ACT tool.
I have been working with MUMmer, and I got the comparison file generated by
MUMmer (using NUCmer function -> .coords file).
as I know, ACT can read the output of MUMmer.
however, when loading the comparison file in ACT, I got error message about
comparison file format.
I don't know which files to use..
Do I need a parser for my MUMmer output files?
If so, could you let me know how I can parse them using Python code?
(I am not a perl person..so if not a complete code, I cannot use them... )
and, I have a one more question..
using ACT tool, can I get the sequences when I selected a part of comparison
region?
Thank you very much for your time,
Sincerely from Sun-Young Lee
-----------------------------------------------------
Sun-Young Lee
Laboratory of Genomics & Genomic Medicine
Lee Gil Ya Cancer and Diabetes Institute
Gachon University of Medicine and Science
Tel : +82 32 899 6545
Fax : +82 32 899 6519
Mobile : +82 19 278 0920
e-mail: sy...@gachon.ac.kr; 209ab...@gmail.com
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