User: johnnytam100

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johnnytam10090
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Posts by johnnytam100

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Comment: C: How to query taxonomy ID using protein accession ID in NCBI or Uniprot?
... Solved. Download from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/ as suggested by Sej Modha [here][1] [1]: https://www.biostars.org/p/276817/#280743 ...
written 6 hours ago by johnnytam10090
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How to query taxonomy ID using protein accession ID in NCBI or Uniprot?
... I want to query a list of taxonomy ID of the proteins using a list of the protein accession ID in NCBI or Uniprot. Does NCBI or Uniprot provide a file which correlates the taxonomy ID, protein accession ID etc. in a table format? Thank you! ...
ncbi taxonomy uniprot written 7 hours ago by johnnytam10090
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Comment: C: How could we compare the extent of evolution between two species?
... Inspiring! I feel exactly the same here that I am mixing up things... If I rephrase my question into a purely technical question: is there a pre-built phylogenetic tree for 16s RNA for all sequenced species? ...
written 2 days ago by johnnytam10090
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Comment: C: What is the standard way of preparing homolog sequences for a phylogenetic analy
... For the outgroup, should it be either 'out' in the sense of 1) blast threshold 2) functional annotation of the protein or 3) both? ...
written 2 days ago by johnnytam10090
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Comment: C: What is the standard way of preparing homolog sequences for a phylogenetic analy
... I see! What could we achieve if we play with the sequence alignment step? ...
written 2 days ago by johnnytam10090
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How could we compare the extent of evolution between two species?
... I have a question in mind and would like to gain insights from biostars members. As the title, for example, if we compare human and a bacteria, generally we will accept a bacteria is 'less evolved' or 'more ancient' or 'more primitive' than human. Then now I have two bacteria, how could we compare ...
evolution written 2 days ago by johnnytam10090
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What is the standard way of preparing homolog sequences for a phylogenetic analysis?
... I have two protein sequences with around 50% identity between them. I want to study the phylogenetic relationship between them. I came up with a method myself: > Step 1: blast each of the sequences to a protein database separately > (possibly with less stringent thresholds) > > Step ...
phylogenetic homolog tree written 2 days ago by johnnytam10090
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Comment: C: Getting loadings of components from pcaMethods
... Good idea! I had a similar thought but does it work for a PCA analysis that we just swap the columns and rows? ...
written 16 days ago by johnnytam10090
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Getting loadings of components from pcaMethods
... I want to get the loadings of components from pcaMethods. To illustrate the problem, I have a matrix `x` a b c 1 ... ... ... 2 ... ... ... 3 ... ... ... By `loadings(pca(x, method="nipals", nPcs=2))`, I get PC1 PC2 a ... ... b ... ... c ... ... However, I ...
pcamethods pca written 16 days ago by johnnytam10090 • updated 16 days ago by Philipp Bayer5.7k
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Package or server to make peptide fragment library for ab initio structural modeling?
... I want to make peptide fragment libraries for ab initio structural modeling of several proteins. I only know [Robetta][1] for this purpose. Could anyone suggest some more packages or web server that do the same thing? I have several proteins thus throughput is a factor. Thanks! [1]: http://r ...
ab initio structural modeling written 18 days ago by johnnytam10090

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Student 19 days ago, asked a question with at least 3 up-votes. For So frustrated compiling necessary packages in a linux system

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