Question

Multiple Sequence Alignment viewers or How to Build a Conservation Plot

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4.5 years ago

Sammy ▴ 20

Hey, I want to get a Conservation Plot across 4 - 5 species. I researched Multiple Sequence Alignment viewers and I encounterd eShadow, zPicture and SeqTools (Belvu). I got different results from eShadow and zPicture (or I have difficulties putting together the results). I am preparing to install SeqTools now. However, for Belvu, I need to prepare the aligned-FastQ file (I am going to use ClustalW) and then upload it in Belvu (as far as I read).

What do you think? Is this the right approach for obtaining a Conservation Plot? Do you have any opinions or preferences on MSA viewers?

RNA-Seq • 2.9k views

ADD COMMENT • link updated 4.5 years ago by h.mon 35k • written 4.5 years ago by Sammy ▴ 20

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I suggest Java-based viewers:

http://genome.lbl.gov/vista/index.shtml

https://www.jalview.org/

https://msa.biojs.net/

A comprehensive list:

https://en.wikipedia.org/wiki/List_of_alignment_visualization_software

This one is only for Windows, but I happen to like it:

http://www.llew.org.uk/chroma/

ADD REPLY • link 4.5 years ago by Mensur Dlakic ★ 27k

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Base-By-Base is on the wikipedia list. (our tool), has several way to summarize the similarity

ADD REPLY • link 4.5 years ago by Cupton ▴ 80

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What is the objective? Do you just want a picture of the alignment?

ADD REPLY • link 4.5 years ago by Joe 21k

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Basically, pretty colours for a PPT. So the conserved region will be obvious for everyone.

ADD REPLY • link 4.5 years ago by Sammy ▴ 20

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My go-to's are usually Jalview, LaTeX (but this requires a bit of work), or, something else you could consider would be to use a sequence logo such as those output by MEME and weblogo.

ADD REPLY • link 4.5 years ago by Joe 21k

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Cheers! Actually I am trying to get started with Jalview right now. It is installed. The newest version 2.11.0. The pink Launch Button from the side is missing. Instead it says to get an installer. I got the installer (I think): Offline Unix shell installer. I cannot find any instructions. I still cannot launch it. Is Jalview still supported?

I also tried to install it with conda but I got errors. I am out of moves:))

ADD REPLY • link 4.5 years ago by Sammy ▴ 20

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It worked with conda afterall.

ADD REPLY • link 4.5 years ago by Sammy ▴ 20

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If you want an alignment with a vintage look, you can use BoxShade.

ADD REPLY • link 4.5 years ago by h.mon 35k

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I got different results from eShadow and zPicture

There are some alternative methods to calculate conservation, so getting different results from different tools doesn't necessarily mean there is something wrong. You have to dig up the method used by each tool, and their default parameters.

I need to prepare the aligned-FastQ file (I am going to use ClustalW)

I don't think ClustalW accepts fastq files, do you mean fasta files?

The EMBOSS suite has the plotcon command-line tool to plot conservation scores. You also have to align the sequences with clustal or other multiple sequence alignment program. Check the thread Calculating Conservation Score From Mutiple Sequence Alignment for some other options.