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Old 10-25-2012, 10:36 PM   #1
GermanGrekhov
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Lightbulb Greatest sequence alignment editor

Hello, scientists!

I have a very big and complex question for you. I want to collect the modern requirements for the greatest sequence alignment editor in the world.

Everybody uses some popular editors, for example JalView, UGENE MSA Editor, BioEdit and other ones. But I think that each person has some own wishes which he/she wants to add into the used tools. Some people resolve such problems using several tools simultaneously (e.g. browser + editor help to fetch sequences from public databases and work with them; or some editor could have a great alignment viewer and another one has a very useful tree viewer). But the handiest way is to have all features available "from the box", collected in one application.

Could you tell me, please, what functionality and usability things you would want to have in the greatest sequence alignment editor in the world?

I think it is interesting for all of you because if such a tool appears it would be great!

Thanks a lot!
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Old 10-28-2012, 08:43 PM   #2
GermanGrekhov
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Is anybody interested in it?
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Old 10-28-2012, 09:07 PM   #3
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A good place to start is by taking a look at Geneious.

Geneious has it flaws, quite a few, but it is one of the most comprehensive tools I've used.

It also allows users to write plugins and thus add functionality that is missing.

Besides the basic functionality, I would like to see Editors that allow a lot of options for creating figures for publications/presentations.
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Old 10-28-2012, 09:10 PM   #4
GermanGrekhov
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Quote:
Originally Posted by chadn737 View Post
A good place to start is by taking a look at Geneious.

Geneious has it flaws, quite a few, but it is one of the most comprehensive tools I've used.

It also allows users to write plugins and thus add functionality that is missing.

Besides the basic functionality, I would like to see Editors that allow a lot of options for creating figures for publications/presentations.
Thanks for the answer. What kind of figures are you talking about? Do you mean special statistics about alignments? Could you list them, please?
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Old 10-30-2012, 08:58 PM   #5
GermanGrekhov
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Your answers is very useful for me. Could anybody else tell something about the topic?
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Old 11-26-2012, 11:02 AM   #6
aprasad
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Several years ago I had a project where I needed to manually edit reasonably large alignments (a few megabases x 40+ species). I had a hard time finding something that made that easy. jalview worked well for moving gaps around, but in some cases I needed to change bases. At the time I don't think they allowed that. JalView might do that now, it was a few years ago. I think I ended up writing a little perl script to modify individual bases. It was a pain.
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Old 11-26-2012, 06:25 PM   #7
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The alignment editor in ARB is pretty nice. It is designed for 16S analysis, but I've also looked at whole genome alignments. You can move gaps, change bases, design primers, etc.

http://www.arb-home.de/
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Old 11-26-2012, 07:26 PM   #8
GermanGrekhov
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Quote:
Originally Posted by aprasad View Post
Several years ago I had a project where I needed to manually edit reasonably large alignments (a few megabases x 40+ species). I had a hard time finding something that made that easy. jalview worked well for moving gaps around, but in some cases I needed to change bases. At the time I don't think they allowed that. JalView might do that now, it was a few years ago. I think I ended up writing a little perl script to modify individual bases. It was a pain.
What goals did you achieve with your script? Was it just simple editing of plain text formats (one-base-replace, insertion, deletion) or it made some special automatic editing of whole alignment data?
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Old 11-26-2012, 10:16 PM   #9
GermanGrekhov
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Quote:
Originally Posted by themerlin View Post
The alignment editor in ARB is pretty nice. It is designed for 16S analysis, but I've also looked at whole genome alignments. You can move gaps, change bases, design primers, etc.

http://www.arb-home.de/
Thank you. Could you tell me please if you need often to edit an alignment manually, or it is very rare thing and you use automatic editor (e.g. muscle-like aligners)?
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Old 11-27-2012, 12:16 AM   #10
RickBioinf
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Quote:
Originally Posted by chadn737 View Post
Besides the basic functionality, I would like to see Editors that allow a lot of options for creating figures for publications/presentations.
I would say for the visualisation of alignment tools, such as BLAST, RDP classifier and RAPSearch, you could use MEGAN. It gives back good looking clado/phylograms and can also look in the KEGG/SEED database for other applications when you are looking at genes. The problem with MEGAN is that it is a payed application and it costs 1200 US$ a year. QIIME is another application it is, according to my opinion, less good looking, but it's free so better for most users.

The downside of these 2 programs is that you can't edit anything in it, because it is just a visualisation tool.

Last edited by RickBioinf; 11-27-2012 at 04:39 AM.
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Old 11-27-2012, 04:47 AM   #11
jiaco
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I would love to see vi extended to handle alignments.

Specifically, searches for sequences and patterns that ignore '-'/gaps and the ability to also find those patterns in reverse complement space.
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Old 11-27-2012, 06:36 AM   #12
aprasad
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Quote:
Originally Posted by GermanGrekhov View Post
Thank you. Could you tell me please if you need often to edit an alignment manually, or it is very rare thing and you use automatic editor (e.g. muscle-like aligners)?
I use automatic aligners, but for some things I needed to edit the sequence manually. First to fix obvious problems in the alignment, and second to replace bases not in the alignment because of obvious errors in the alignments / assemblies. Sometimes by looking at the multiple sequence alignment it is obvious that the aligner or assembler made a mistake.

Anyway, I haven't needed this in a long time, and probably most people don't bother to manually edit their alignments anymore since it is quite tedious with very large sequence sets.

I'm going to check out ARB. I hadn't heard of it before.
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Old 11-28-2012, 07:42 PM   #13
GermanGrekhov
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I have tried ARB and can say that it is a very complex tool without good user friendly interface. I don't understand how to look through an alignment in this program, it just shows me phylogenetic trees.
Also, it was very hard to make it runnable on Ubuntu.
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Old 11-29-2012, 06:56 AM   #14
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Quote:
I have tried ARB and can say that it is a very complex tool without good user friendly interface. I don't understand how to look through an alignment in this program, it just shows me phylogenetic trees.
Also, it was very hard to make it runnable on Ubuntu.
Yes, it is hard to install. When you run ARB, click on 'CREATE and IMPORT'. Find your own alignment, click 'auto detect', and select fasta_wgap, then go. There will be a list of all of the reads in your alignment. Then click the Tab that looks like an EXCEL spreadsheet - this will launch the alignment editor. If you click 'More Sequences', you will see your alignment. You will have to adjust the protection level in order to manipulate your reads from there.

J
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