User: alexille5640

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alexille564010
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Posts by alexille5640

<prev • 18 results • page 1 of 2 • next >
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UCSF Chimera Inter-Helical Angle Calculation?
... When using UCSF Chimera you have the option to retrieve the "crossing angle" between two alpha-helices of a protein structure. (This is done by clicking Tools > Structure Analysis > Axes/Planes/Centroids > Define Axes). What does this this "crossing angle" represent? How is it calculated b ...
protein structure chimera protein prediction written 3 months ago by alexille564010 • updated 3 months ago by WouterDeCoster38k
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Mixed population of cells - Targeted / Amplicon Sequencing?
... I have the following: - SAMPLE 1: a culture of normal unmodified HEK293 cells (a pure population where all cells are the same) - SAMPLE 2: a culture of HEK293 cells on which I did a custom gene knock in via CRISPR and homology directed repair. (after a 90%+ transfection rate, only about 3% of cel ...
gene next-gen sequencing written 4 months ago by alexille564010
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Mouse Myelin Basic Protein Promoter Sequence?
... I am having trouble identifying/locating the MBP promoter sequence for Mus musculus (mouse). According to [this article][1] the promoter is 1.3kb in length. However, I can't seem to locate the sequence itself anywhere online. Once found, I want to be able to confirm this sequence by locating it wi ...
genome gene sequence written 5 months ago by alexille564010 • updated 5 months ago by genomax65k
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Comment: C: How accurate is UniProt?
... The degeneracy, used to describe how one Amino Acid can be encoded by multiple codons. ![Codon Table][1] [1]: https://www.mun.ca/biology/scarr/MGA2-03-28_mtDNA_code.jpg ...
written 5 months ago by alexille564010
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Comment: C: How accurate is UniProt?
... Sorry for my lack of knowledge, but how do you access the corresponding nucleotide entry of for example: Mus musculus Actin Beta entry from uniprot (https://www.uniprot.org/uniprot/P60710). ...
written 5 months ago by alexille564010
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Comment: C: How accurate is UniProt?
... Yes, relying on the degeneracy of codons, I'm assuming "Sequence Manipulation Suite: Reverse Translate" is sufficient. ...
written 5 months ago by alexille564010
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How accurate is UniProt?
... I am curious about the reliability of Uniprot amino acid sequences? Say I want to do the following: 1. Reverse translate a reviewed Uniprot amino acid sequence into a nucleotide sequence (using [Sequence Manipulation Suite Reverse Translate][1]) 2. Synthesize that nucleotide sequence in vitro in ...
gene genome sequence sequencing written 5 months ago by alexille564010 • updated 5 months ago by WouterDeCoster38k
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Comment: C: mRNA transcript sequence analysis
... Thank you for clarifying this! I am very grateful. ...
written 9 months ago by alexille564010
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mRNA transcript sequence analysis
... By convention, i understand that when a mRNA sequence is obtained, it is automatically formatted as cDNA for computational analysis. (the U nucleotide is automatically formatted as T) I am having trouble finding publications which illustrate mRNA sequence analysis in text or in figures showing conv ...
mrna cdna written 9 months ago by alexille564010 • updated 9 months ago by h.mon24k
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CHIMERA Protein Structure Positioning Question
... Say I have a protein structure consisting of multiple alpha-helices. How do I select one alpha-helix and position the entire protein so that this one alpha helix is perfectly vertical, or horizontal? ...
protein structure chimera written 10 months ago by alexille564010 • updated 10 months ago by jrj.healey11k

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