User: nobu.kim66

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nobu.kim6610
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Posts by nobu.kim66

<prev • 12 results • page 1 of 2 • next >
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(Closed) De novo sequencing homework question, what is the parent peptide mass?
... [imglink][2] In that example, 129+216+327 does not equal the parent's mass of 492. My understanding is that during MS, the protein is broken down into peptide masses of varying length of approx. 5 to 20 amino acids. They also lose ions such as water or ammonia like in the example., the experimen ...
spectrometry written 10 hours ago by nobu.kim6610
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Comment: A: Biopython tools online
... What are internal, target, query? ...
written 8 days ago by nobu.kim6610
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Comment: A: Biopython tools online
... @Joe, we are starting with implementing our own Needleman and Waterman with a Plotly Dash frontend. Unfortunately, our group stumbled on Needleman so was looking at using: 6.6.2 PairwiseAligner The new Bio.Align.PairwiseAligner implements the Needleman-Wunsch, Smith-Waterman, Got ...
written 8 days ago by nobu.kim6610 • updated 8 days ago by ATpoint42k
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Biopython tools online
... Hello, For a school project, my group and I were thinking of making a full suite of Biopython tools available via a web interface (no coding necessary by users). Would there be any demand for this kind of website? Or would it be redundant since there is Emboss? ...
biopython written 8 days ago by nobu.kim6610
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Comment: C: what is * in the NCBI Blosum and PAM matrices
... that's what I thought too, but maybe better to return some error message to the user in case that does happen (alongside any alignments) ...
written 8 days ago by nobu.kim6610
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what is * in the NCBI Blosum and PAM matrices
... # Matrix made by matblas from blosum45.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/3 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= 45 # Entropy = 0.3795, Expected = -0.2789 A R N D C Q ...
matrix blosum pam written 9 days ago by nobu.kim6610
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What are the main differences between NCBI, EBI and DBBJ?
... I'm taking an intro class and read that they exchange sequences daily so in terms of data they are equivalent but each site has some differences with regards to features and built-in programs. What are the main differences, pros and cons? ...
database written 14 days ago by nobu.kim6610 • updated 14 days ago by Jean-Karim Heriche23k
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Comment: C: Turning Seq objects into strings
... Not really @joe. He might be a biologist and not a programmer like yourself and I. seq1 = SeqIO.read("example_fasta_files/homo_sapiens_lactate.fasta", "fasta") print(type(seq1.seq)) #this is the seq attribute of the seq1 object strrep = str(seq1.seq) #so cast the seq attribute to str ...
written 17 days ago by nobu.kim6610
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Error using NCBI Python guide
... Found here: https://www.ncbi.nlm.nih.gov/dbvar/content/tools/entrez/ I get KeyError Traceback (most recent call last) in ----> 1 for ds in dsdocs['eSummaryResult']['DocumentSummarySet']['DocumentSummary']: 2 for p in ds['dbVarPlacemen ...
python api entrez written 23 days ago by nobu.kim6610 • updated 23 days ago by _r_am31k
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Answer: A: how to measure similarity from EMBOSS Needleman output
... Thanks! That really clarifies it for me. ...
written 4 weeks ago by nobu.kim6610

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