Multiple sequence alignment images
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3 months ago
alslonik ▴ 310

Hi all, For my online database I need to produce a batch of coloured multiple sequence alignment images (pdf or png ore any other image is good) of the sequences and the alignments that I have in fasta files. I use "ggmsa" R package now, but it is good for presenting relatively short alignments and mine are >1000 AA. Is there any other R library that can produce something like this? Or ther software that can produce batches of alignments in coloured image format?

MSA R ggmsa Jalview • 553 views
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I've used UGENE to do this. I think for 1k length it will work okay. It's a bit tricky to visualise such a long alignment. Is there something you want to show?

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I want to show orthologous sequences of proteins in different species. So, the sequence is of the whole protein.

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sounds like you want a circos plot or similar https://circos.ca/

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As far as I understand circos is good for aligning genomes and proteomes. I just want to show linear protein alignment of a number of orthologous and paralogous proteins. Meaning, something like jalview with an option to process batches of thousands of alignments.

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I'll look into it, thanks for your answer, Mark!

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