User: manaswwm
manaswwm • 130
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Posts by manaswwm
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... Thanks for your suggestion, Elisabeth!
I realized I can also do this much later, what I ended up doing is using Uniprot's REST API service to convert my ensembl gene id to uniprot protein id - https://www.ebi.ac.uk/proteins/api/doc/#!/proteins/getByCrossReference (here I set dbtype - EnsemblPlants ...
written 5 weeks ago by
manaswwm • 130
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... I am running this on a Debian system, to make things easier to understand, here is the sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)
Matrix products: default
BLAS/LAPACK: /home/mjoshi/De ...
written 12 weeks ago by
manaswwm • 130
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... Hi Kevin,
thanks for your answer. I agree this would be an efficient way of doing things instead of sending in requests one at a time, however, the point that I would like to make is that I am not able to send in any requests at the moment. For example, even when I run your code I still get the same ...
written 12 weeks ago by
manaswwm • 130
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... Hello everyone,
I have been using biomaRt for some time now and it has been working nicely. However, today while trying to convert some ensembl gene ids to uniprotswissprot ids I have been facing some problems. The code and the error are as follows:
#importing the library
library(biomart)
...
written 12 weeks ago by
manaswwm • 130
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... I know this is possible the following way in R using biomaRt : pdb id - gene id - GO annotation (cellular colocalization). Python also has biomart package https://pypi.org/project/biomart/ however I have not tried this in python, however should be doable ...
written 3 months ago by
manaswwm • 130
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... Ah, so you already have a gene sequence where all exons are merged together and you want to "separate" those exons? And then translate them to their individual amino acid sequences?
I think this should be straightforward if you know the annotations, so you know how many exons you have, which one com ...
written 4 months ago by
manaswwm • 130
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... I am not sure if I fully understand your question but I think it would looklike -
5' UTR -- CDS domain 1 (72 nucleotides, 24 AA) -- intron sequence -- CDS domain 2 (269 nucleotides, this is not a multiple of 3, you may be missing one more nucleotide position?)
When this gene is processed - the intr ...
written 4 months ago by
manaswwm • 130
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... this can be done in the following steps:
- import the sequence using Biopython (*SeqIO.read()*)
- import the excel file as table using pandas, subset the table to only keep the start and stop positions
- go through the columns of this table in a for loop, splice the sequence using start and stop col ...
written 5 months ago by
manaswwm • 130
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... have you tried using biomaRt in R? more on this package and examples - https://bioconductor.statistik.tu-dortmund.de/packages/3.3/bioc/vignettes/biomaRt/inst/doc/biomaRt.pdf. ...
written 5 months ago by
manaswwm • 130
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... have you considered doing MSA on the multiple specific regions of interest. For example, doing MSA on all annotated protein coding regions in the reference genome against your 1800 genomes? I think the protein coding regions would be smaller than the limit for most softwares, and you can also run th ...
written 5 months ago by
manaswwm • 130
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Teacher
20 months ago,
created an answer with at least 3 up-votes.
For C: network visualization (multiple data source integration)
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