I need help in this
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6.9 years ago
efosa15 • 0

Op is having problems with weblem 5-6 on growth hormones: https://global.oup.com/uk/orc/xedition/leskbioinf4exe/student/weblems/ch05/#

How do I go about it?

gene weblems alignment • 1.6k views
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Sorry, I had to delete the content of the question, because of potential copyright violations. If you can't rephrase the task in your own words, you should consider that you are not up to solving this task (yet).

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Wow! Tot it was my school alone. Hmm!

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Another option would be to simply read the Chapter of the book: Chapter 5: Sequence alignments and phylogenetic trees.

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Ok. Thanks for that, really appreciate but followed the link but I can't really lay my hands on the text book, would I have to buy it please?

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So, please how do I go about it, know I have to do multiple sequence alignment and also generate phylogenetic trees. My problem is laying my hands on the amino acids, before doing a MSA or is there a better way to go about it? Thanks.

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They want you to make a simplified standard phylogeny:

  1. pick homologs
  2. msa
  3. phylogenetic tree, compare branch lengths

The first step is the most time consuming one (unless you want to run MrBayes with 5 million iterations;). If you don't know anything about a gene, google/wikipedia it. There you can read a bit about the function, most wikipedia articles on genes and proteins will have links to sequence databases (e.g. Uniprot). Most sequence databases have a Blast feature, find some hits in our closest relatives. Since Darwin's times we know what are the closest relatives to humans and add an outgroup, done. Now I have already said too much ;)

The rest is easy, any phylogentic method will do fine for such a large effect.

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Thank you so much sir, really appreciate your help.

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Sir, would I also do this same process for weblems 5-11? Thanks in anticipation and also for the first question.

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Similar but not identical approach. The search for homologs is constrained to Mt genes. It will be easier to get all mitochondrial proteins from a dedicated resource in ncbi. Using 12 proteins suggests that we either build 12 trees and then make a consensus tree or use concatenated alignments. Also, it looks like the outcome would depend a bit more on the phylogenetic methods this time, and the hypothesis is more complex. Therefore I'd try more advanced phylogenetic methods like ML and Bayesian.

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Ok sir. Thank you so much, love the challenge but all this looks complex for someone just weeks old in the field of Bioinformatics. Anyway thank you so much sir really appreciate your help.

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I agree, 5-11 is no longer beginner level.

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Hmm, thanks so much I believe my lecturer is challenging us. Thanks for your help sir.

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homework?

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yes but don't know how t go about it. just started bioinformatics. been online all tru.

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Yes I did, that was before I was shown how to go about it. Is doing that wrong? if it is I'm very sorry about it. Thanks.

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Hello efosa15!

We believe that this post does not fit the main topic of this site.

Homework question

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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