User: manaswwm

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manaswwm130
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Posts by manaswwm

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Answer: A: biomaRt error while converting ensembl gene Id to uniprot ID
... 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 manaswwm130
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Comment: C: biomaRt error while converting ensembl gene Id to uniprot ID
... 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 manaswwm130
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Comment: C: biomaRt error while converting ensembl gene Id to uniprot ID
... 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 manaswwm130
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biomaRt error while converting ensembl gene Id to uniprot ID
... 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) ...
R biomart uniprot ensembl written 12 weeks ago by manaswwm130
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Comment: C: map protein structure to cellular location through their pdb id
... 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 manaswwm130
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Comment: C: convert CDS coordinates of a GTF to amino acid coordinates respect the resultant
... 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 manaswwm130
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Comment: C: convert CDS coordinates of a GTF to amino acid coordinates respect the resultant
... 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 manaswwm130
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Comment: C: How to retrive sequnce from fasta file by using start and end point data from xl
... 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 manaswwm130
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Comment: C: Programmatically get compounds in ChEMBL from related targets
... 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 manaswwm130
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Comment: C: Multiple Sequence Alignment for Full length genomes
... 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 manaswwm130

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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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