Question: Multiple Sequence Alignment viewers or How to Build a Conservation Plot
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gravatar for Sammy
5 weeks ago by
Sammy10
Sammy10 wrote:

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 • 210 views
ADD COMMENTlink modified 5 weeks ago by h.mon28k • written 5 weeks ago by Sammy10
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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 REPLYlink written 5 weeks ago by Mensur Dlakic2.2k
1

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

ADD REPLYlink written 5 weeks ago by Cupton70

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

ADD REPLYlink written 5 weeks ago by Joe15k

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

ADD REPLYlink written 5 weeks ago by Sammy10
1

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 REPLYlink modified 5 weeks ago • written 5 weeks ago by Joe15k

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 REPLYlink written 5 weeks ago by Sammy10

It worked with conda afterall.

ADD REPLYlink written 5 weeks ago by Sammy10
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If you want an alignment with a vintage look, you can use BoxShade.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by h.mon28k

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.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by h.mon28k

Yest. I meant fasta. Thank you.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by Sammy10
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