That's a good observation and idea, and it makes sense!
No, I haven't yet tried the predicted protein sequences. I will try that route. Thank you swbarnes2
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If they differ in length that much, there probably isn't one easy way to align them, and that's why you are getting different answers. Have you tried aligning the predicted protein sequences? Those will likely be more similar than the DNA sequences. And in the end, you probably care most about teh amino acid changes anyway.Leave a comment:
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Which Sequence aligners to use?
Hello wise people,
I'm trying to align a sequence of a gene that is present in two related species. Each of the genes in either species has SNPs in various positions. My goal is to find if the SNPs are in similar positions, or better yet align with each other.
In one species the length is ~700 bases and the other ~1200bases.
I didn't know how to go about with it, so with trial and error, I tried using different aligners [clc, bioedit (pairwise alignment, global and clustalw), muscle]...and they are all giving me different results.
I was just wondering what might be causing the differences because I am presuming I am doing something wrong.
Which other aligners would you suggest I use for this. Should I do global alignment or local alignment?
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Differential Expression and Data Visualization: Recommended Tools for Next-Level Sequencing Analysis
After covering QC and alignment tools in the first segment and variant analysis and genome assembly in the second segment, we’re wrapping up with a discussion about tools for differential gene expression analysis and data visualization. In this article, we include recommendations from the following experts: Dr. Mark Ziemann, Senior Lecturer in Biotechnology and Bioinformatics, Deakin University; Dr. Medhat Mahmoud Postdoctoral Research Fellow at Baylor College of Medicine;...05-23-2023, 12:26 PM -
Continuing from our previous article, we share variant analysis and genome assembly tools recommended by our experts Dr. Medhat Mahmoud, Postdoctoral Research Fellow at Baylor College of Medicine, and Dr. Ming "Tommy" Tang, Director of Computational Biology at Immunitas and author of From Cell Line to Command Line.
Variant detection and analysis tools
Mahmoud classifies variant detection work into two main groups: short variants (<50...05-19-2023, 10:03 AM -
With new tools and computational resources being released regularly, it can be hard to determine which are best suited for the analysis process and which older tools continue to be maintained. In an effort to assist the sequencing community, we interviewed three highly skilled bioinformaticians about their recommended tools for several important analysis applications.
Quality control and preprocessing tools
“Garbage in, garbage out” is a popular...05-16-2023, 10:11 AM
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