User: biohacker_tobe
biohacker_tobe • 40
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Posts by biohacker_tobe
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... I have done the aligning of my protein sequences and of short reads against a protein reference database using diamond. However I would like to annotate my alignments but I would prefer to do this on bash. I found this https://resources.qiagenbioinformatics.com/manuals/clcmgm/current/index.php?manua ...
written 3 months ago by
biohacker_tobe • 40
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Comment:
C: Gene Cluster Phylogenetic Tree
... Yes i was, I can share my code but it's on R ...
written 3 months ago by
biohacker_tobe • 40
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... It was not executing since I am using a fish shell, I needed to add the bash command in front in order for it to run:
bash -c 'for acc in `cat protein_ids.txt` ; do curl -s "https://www.uniprot.org/uniprot/$acc.fasta"; done > uniprot_seqs.fasta' ...
written 5 months ago by
biohacker_tobe • 40
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... running this from my command line:
for acc in `cat uniprot_ids.txt` ; do curl -s "https://www.uniprot.org/uniprot/$acc.fasta" ; done > uniprot_seqs.fasta
does not actually do anything :s I have the file saved exactly as listed. it just stays in one state. ...
written 5 months ago by
biohacker_tobe • 40
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... I saw that this uses linux command directly, was curious if I could do it directly from a python command. ...
written 5 months ago by
biohacker_tobe • 40
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... I have a list of protein id's, these all traceback to Uniprot. However, I wanted to know if I can obtain sequence information from these proteins from uniprot protein ids.. Is there any package in biopython to do this?
I found this snippet of code online and it does give the sequence information bu ...
written 5 months ago by
biohacker_tobe • 40
• updated
5 months ago by
Shalu Jhanwar • 490
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... Thanks, this is exactly what I was looking for :D ...
written 5 months ago by
biohacker_tobe • 40
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... Fair enough, thanks for the pointer :) ...
written 5 months ago by
biohacker_tobe • 40
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... With linux I am aware on how to do it, but is it possible directly with python? ...
written 5 months ago by
biohacker_tobe • 40
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... For example, is it possible to get the organism name as one gets the sequence and gene id for example:
>sp|Q09305|AAR2_CAEEL Protein AAR2 homolog OS=Caenorhabditis elegans GN=F10B5.2 PE=3 SV=1
MGGALPPEIVDYMYRNGAFLLFLGFPQASEFGIDYKSWKTGEKFMGLKMIPPGVHFVYCS
IKSAPRIGFFHNFKAGEILVKKWNTESETF ...
written 5 months ago by
biohacker_tobe • 40
• updated
5 months ago by
Joe ♦ 18k
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