User: yamule

gravatar for yamule
yamule120
Reputation:
120
Status:
Trusted
Location:
Japan
Website:
https://github.com/yamule
Last seen:
1 day, 1 hour ago
Joined:
11 months, 3 weeks ago
Email:
k***************@gmail.com

Hobbyist.

Working for a commercial company but this & github account are managed for private purpose.

Posts by yamule

<prev • 34 results • page 1 of 4 • next >
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Answer: A: How to extract and calculate all protein atom to ligand atom distances from pdb
... I think the main problems of the script are if ($line =~ /^HETATM/) { $part++; next; } and elsif ($part ==1){ push @points, [ @array ]; } If HETATM label is found, it will go to the first line of the "while" loop (because of "next") and no elemen ...
written 4 days ago by yamule120
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Answer: A: Deleting constant site columns OK?
... No. Because the columns have information. It'll change branch length of the phylogenetic tree at least. ...
written 6 weeks ago by yamule120
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Comment: C: Looking for a pdb file of HIV-1 Protease without any inhibitors or substrate
... What are the exact residues in the active site? ...
written 7 weeks ago by yamule120
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Comment: C: Mutation and Energy minimzation by using modeller
... It's not an error message related to modeller. It's more general pyton error. Did you installed multiple python distribution? Or unknown things happened. anyway your python seems to be broken. Uninstall python and reinstall it or using Anaconda ( https://www.anaconda.com/ ) may work. (Btw, I recomme ...
written 7 weeks ago by yamule120
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Comment: C: Mutation and Energy minimzation by using modeller
... I think it is good to copy and paste command you made and error messages you got. ...
written 7 weeks ago by yamule120
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Answer: A: Finding ortholog genes
... Reciprocal best hit approach is the simple and easy way. (if you have whole gene sequences coded in the sorghum genome). https://www.google.co.jp/search?q=reciprocal+best+hit ...
written 11 weeks ago by yamule120
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Comment: C: E-value results from hmmsearch are not accurate. [HMMER]
... You are using "negative" dataset? Does it mean your hypothesis is that there are histone avoiding motifs in the dataset and you were going to model Histone avoiding motif with HMM? It is very interesting. I'm not a nucleotide person and have not used HMMER or MUSCLE so much, following comments are ...
written 11 weeks ago by yamule120
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Comment: C: local blast on ubuntu 17.04 using refseq_genomic
... "in" must be "-in", I think. ...
written 12 weeks ago by yamule120
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Comment: C: E-value results from hmmsearch are not accurate. [HMMER]
... Are you sure that those nucleotide entries in your fasta are from the same family, the same super family or the same fold that you want to make profile? I googled the names of the entries and found that they have various descriptions which I thought they must belong to different families (SUL1 and S ...
written 12 weeks ago by yamule120
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Comment: C: E-value results from hmmsearch are not accurate. [HMMER]
... In the output of hmmbuild, "eff_nseq" is too high and "re/pos" is too low. I think that is because your input multi-FASTA file is not aligned and resulting hmm is nonsense. Thus does not hit against any sequence. ...
written 12 weeks ago by yamule120

Latest awards to yamule

Autobiographer 12 weeks ago, has more than 80 characters in the information field of the user's profile.
Scholar 7 months ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction

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