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3.0 years ago
anikcropscience
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230
Hello, I have several questions regarding multiple sequence alignment (MSA):
- How can I produce publication-quality MSA figure for 150 samples? At the moment, I am using JalView for viewing the alignments. I do not plan to show every detail of the alignments. I can just select a part from the whole figure and zoom it to show the main result. I have a section of an MSA file for a specific gene sequence like this below
Is it possible to detect the presence of any structural variation from an MSA file like the above? Because I see that people only detect single nucleotide polymorphisms from such alignments.
I am planning to make a figure by keeping the alignment view and the phenotypic result side by side. I have an ordered histogram for the phenotype that the gene is responsible for and I want to sort the alignments according to their phenotypic value. Is there any tool to integrate such datasets and produce a joint figure? Because I want to keep the samples in order according to their phenotypic value.
Please let me know if you have any suggestions on those questions.
Thank you.
