User: fishgolden

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fishgolden420
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Posts by fishgolden

<prev • 109 results • page 1 of 11 • next >
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Comment: C: Is BLAST highly sensitive?
... > I mean there is whole genome and there is my mRNA which is transcribed from a gene and this gene is in the genome so why can't I find any similarities ? I might misunderstand what you are talking but, the genome of *Hypsibius dujardini* looks that is not booked in refseq_genomes db. I think ...
written 5 weeks ago by fishgolden420
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Comment: C: Is BLAST highly sensitive?
... > So is this totally normal? Yes. Searching similar nucleotide sequences are really difficult because there are only 4 different types of letters in general. Which variants of BLAST did you use? Using tblastx https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastx&PAGE_TYPE=BlastSearch& ...
written 5 weeks ago by fishgolden420
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Comment: C: Protein of un-clear function
... At first, you have to make sure that the translated amino acid sequence is the same as you expected and then you can perform sensitive search like [hhsuite][1] and [hmmer][2] [1]: https://github.com/soedinglab/hh-suite [2]: http://hmmer.org/ ...
written 3 months ago by fishgolden420
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Comment: C: Protein of un-clear function
... Hmm all blast hits I can see are hypothetical or predicted proteins... It's quite dangerous to proceed without evidence that the gene is really expressed and translated. ...
written 3 months ago by fishgolden420
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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 3 months ago by fishgolden420
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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 3 months ago by fishgolden420
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Comment: C: Predict function by Mutation?
... googling > loss of function mutation database may also be helpful. ...
written 6 months ago by fishgolden420
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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 6 months ago by fishgolden420
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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 9 months ago by fishgolden420
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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 9 months ago by fishgolden420

Latest awards to fishgolden

Centurion 9 months ago, created 100 posts.
Scholar 10 months ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction
Scholar 14 months ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction
Popular Question 16 months ago, created a question with more than 1,000 views. For (solved) I couldn't reproduce the problem of max_target_seqs
Supporter 17 months ago, voted at least 25 times.
Scholar 17 months ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction
Scholar 19 months ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction
Student 20 months ago, asked a question with at least 3 up-votes. For (solved) I couldn't reproduce the problem of max_target_seqs
Autobiographer 2.7 years ago, has more than 80 characters in the information field of the user's profile.
Scholar 3.1 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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