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Old 04-27-2012, 06:23 AM   #1
Antony03
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Default Software like consed

Hi everyone!

I'm looking for a software like consed for visualize alignment and editing the consensus sequence. At my work, I have a MAC with consed on it, but at home I have a PC with windows 7 and consed is unavailable on this platform.

I downloaded Tablet, it looks nice but I don't know how, and if I can, change the consensus.

Thanks
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Old 04-27-2012, 07:19 AM   #2
maubp
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Tablet is a viewer, not an editor.

You could also consider Gap5 which is a full assembly editor, but that doesn't work on Windows.

If you really want to work on your home computer, install Linux Or if you have a good internet connection, perhaps try an X Windows client to connect to a Linux/Unix server at work?
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Old 04-27-2012, 07:27 AM   #3
Antony03
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I think I will install linux! Have you an idea of which distribution?
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Old 04-27-2012, 07:45 AM   #4
maubp
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Quote:
Originally Posted by Antony03 View Post
I think I will install linux! Have you an idea of which distribution?
That is a quite subjective question, but if you want to use this primarily for Bioinformatics, then going with the Debian based Bio-Linux distribution would seem sensible:
http://nebc.nerc.ac.uk/tools/bio-linux/bio-linux-6.0

The appeal here is so many major tools are then simple to install, and generally quite up to date too (via Debian-Med):
http://nebc.nerc.ac.uk/tools/bioinfo...throughput-seq

You could opt for another Debian based distribution and use Debian-Med directly too:
http://www.debian.org/devel/debian-med/

To be honest - I'd suggest using whatever your local Linux using friends use, so that you have someone nearby who can help out if needed, rather than having to resort to the internet.
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Old 04-27-2012, 01:50 PM   #5
Antony03
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Hi! I downloaded a linux distrubution and gap5. I don't understant how create a database. Is there a person who can help me? I know I need this code: tg_index -o dbname [options] -format_code input_filename, but not where I need to write this! Sorry, I'm new with that kind of software.
Thanks

Last edited by Antony03; 04-27-2012 at 06:33 PM.
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Old 04-28-2012, 05:26 PM   #6
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Hi! Sorry for the double post! Is somebody can help me with my problem? I really need to know how to create a database with .ace as input for use in Gap5. It's for my master.

Thanks
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Old 04-29-2012, 04:02 AM   #7
maubp
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Have you searched the forum? There are other threads about installing Gap5.
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Old 04-29-2012, 05:54 AM   #8
Antony03
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Yes sure! http://seqanswers.com/forums/archive...hp/t-1923.html
I know I need to do something with tg_index, but what I don't understand it how to use it for create a .g5d and .g5x with a .ace as input.

It tg_index a plugin or something like this? Is there another manner for convert a .ace in .g5d?

I know my question is a little bit stupid, but i'm new in this domain
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Old 04-29-2012, 02:50 PM   #9
Antony03
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I followed this tutorial for the installation on Ubuntu http://tygertown.us/2011/03/install-...buntu-mavrick/. But, after, what I need to do?
For convert my .ace in .g5d, I need to launch tg_index in wich directory?
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Old 05-06-2012, 05:56 PM   #10
AdrianP
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Use Geneious.
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Old 05-10-2012, 01:58 AM   #11
jkbonfield
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Quote:
Originally Posted by Antony03 View Post
Yes sure! http://seqanswers.com/forums/archive...hp/t-1923.html
I know I need to do something with tg_index, but what I don't understand it how to use it for create a .g5d and .g5x with a .ace as input.

It tg_index a plugin or something like this? Is there another manner for convert a .ace in .g5d?

I know my question is a little bit stupid, but i'm new in this domain
Firstly, Gap5 does work natively on Windows too, but it's not really optimised for the platform. Specifically tg_index is a command line tool used to build the gap5 database, but a command line is complete anathema to windows users! (It works though in exactly the same manner as linux, you just have to launch a console window to run it from.)

I plan to putting tg_index into gap5 itself so you can also build databases via the GUI, albeit then having to wait a long while potentially on a large DB. That's not done yet though.

As to using tg_index, just try "tg_index" on a command line to see the options. In the most common usage you could just do "tg_index filename.ace" and get a filename.0 gap5 database spat out at the end, but there are various command line options for controlling it further.
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