User: fishgolden

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fishgolden450
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Posts by fishgolden

<prev • 115 results • page 2 of 12 • next >
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Comment: C: Protein of un-clear function
... Have you performed wet experiments? I think standard way to investigate function of gene is check expression -> check translation -> check localization, knock down analysis etc.. ...
written 6 months ago by fishgolden450
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Comment: C: Protein of un-clear function
... The alignments with CDD domains look false positive for me because only a partial (non-repeat) region is matched with the repeat region. ...
written 6 months ago by fishgolden450
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Comment: C: Predict function by Mutation?
... googling > loss of function mutation database may also be helpful. ...
written 9 months ago by fishgolden450
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Answer: A: predicted protein and sequence
... I use uniprot for such purpose. It has PE line. https://www.uniprot.org/docs/userman.htm#PE_line Check an example. https://www.uniprot.org/uniprot/Q8YW84.txt ...
written 9 months ago by fishgolden450
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Answer: A: biopython.PDB residue.get_id() does not match sequence index
... I'm not using biopython but as I thought this is one of the general pit fall of handling PDB structure, I give an answer. (please give a comment if it isn't) Why idx and id are different is because "id" means not "index" but "identifier". Residues in PDB have several ids. There are two such ids at ...
written 12 months ago by fishgolden450
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Comment: C: Multiple alignment software
... They are amino acid sequences thus they must be reverse translated into nucleotide when you benchmark nucleotide alignment software. Then it becomes codon-based alignment benchmark (the gaps are placed between two codon frames. It's quite biased.) & It can not be applied to aligning SINE. ...
written 12 months ago by fishgolden450
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Comment: C: Multiple alignment software
... https://www.ncbi.nlm.nih.gov/pmc/articles/PMC29792/ BaliBASE is from proteins which have 3D structure... Nucleotide people may use it for benchmarking algorithms, however, it's not suitable for his analysis, at least.... ...
written 12 months ago by fishgolden450
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Comment: C: Local protein BLAST not working
... Isn't it that you should give to "query=" arg, instead of raw amino acid sequence? ...
written 12 months ago by fishgolden450
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Answer: A: Multiple alignment software
... At a glance, I thought that all alignments are nonsense. I wouldn't do any downstream analysis with any of those alignments. However, if you want to discuss about the accuracy of algorithms; T-Coffee, Clustal Omega, and yours, you should evaluate those algorithms with some benchmark dataset. I'm ...
written 12 months ago by fishgolden450
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Comment: C: How to create PSSM matrix
... "I have downloaded this as a pssm" It's ASN.1 format. You can use it as input file of sofware/web-service in my answer. I can't see needed format[1] yet. ...
written 12 months ago by fishgolden450

Latest awards to fishgolden

Centurion 12 months ago, created 100 posts.
Scholar 13 months ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction
Scholar 16 months ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction
Popular Question 18 months ago, created a question with more than 1,000 views. For (solved) I couldn't reproduce the problem of max_target_seqs
Supporter 20 months ago, voted at least 25 times.
Scholar 20 months ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction
Scholar 22 months ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction
Student 23 months ago, asked a question with at least 3 up-votes. For (solved) I couldn't reproduce the problem of max_target_seqs
Autobiographer 2.9 years ago, has more than 80 characters in the information field of the user's profile.
Scholar 3.4 years ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction

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