User: darkmatter1996

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Posts by darkmatter1996

<prev • 8 results • page 1 of 1 • next >
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Stanford HIV-DB Sequence does not match with reference
... I am trying to analyze data from the Stanford HIV-db. However, it appears that the data for NRTIs and NNRTIs (for example this file https://hivdb.stanford.edu/download/GenoPhenoDatasets/NRTI_DataSet.txt) contain data for 240 amino acids, while the consensus sequence for reverse transcriptase (found ...
hiv written 6 months ago by darkmatter19960
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Phylogenetic Trees of HLA class I alleles
... I am running an experiment in which I need to compare the similarity of HLA alleles. To do this, I was thinking of looking for a phylogenetic tree of the HLA alleles. However, the only references I was able to find are from 1999: https://academic.oup.com/mbe/article/16/2/147/1018331/Locus-specificit ...
hla written 18 months ago by darkmatter19960
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Comment: C: Dataset containing all HLA class I alleles
... I have not. How would I get this kind of data from there? Could you please explain a bit more. ...
written 18 months ago by darkmatter19960
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Dataset containing all HLA class I alleles
... I am running an experiment in which I need to sample all six HLA class I alleles (HLA-A, HLA-B, HLA-C) repeatedly. Is there a dataset online that contains this information? I found this website (http://www.allelefrequencies.net/) but I cannot figure out how to get the data from it in the format that ...
hla written 18 months ago by darkmatter19960 • updated 17 months ago by Biostar ♦♦ 20
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Comment: C: Cannot install ATHLATES, issues with bamtools
... No, sorry, I meant the Athlates installation. I updated the previous comment. ...
written 19 months ago by darkmatter19960
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Comment: C: Cannot install ATHLATES, issues with bamtools
... I'm aware of that. The issue is that the Athlates installation is failing, and that appears to be because the files are not in the right place, as the include directory does not exist, and the lib directory is empty. Sorry if that was not clear from the OP. I'm asking if anyone knows why this is hap ...
written 19 months ago by darkmatter19960
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Cannot install ATHLATES, issues with bamtools
... I am trying to install Athlates (July 31, 2014 version) from the instruction here: https://hpc.nih.gov/docs/Athlates.pdf on a computing cluster. However, I am running into issues with the corresponding bamtools. The Athlates makefile echoes the following command: /usr/bin/g++ -O3 -I/n/home05/ae ...
software error written 19 months ago by darkmatter19960
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Does sgRNA have to be complementary to DNA strand?
... I have been analyzing the data from the Xu et. al (2015) paper (see Supplemental Table_1.xlsx [here][1]). However, it appears that many of the sgRNAs shown are not complementary to any part of the targeted gene indicated. For example, I downloaded the NCBI sequence data for the gene RPL17, and was n ...
python sgrna written 2.4 years ago by darkmatter19960

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