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User: biohacker_tobe

gravatar for biohacker_tobe
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Posts by biohacker_tobe

<prev • 63 results • page 1 of 7 • next >
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How to annotate Diamond output files
... 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 ...
alignment written 19 days 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 19 days ago by biohacker_tobe • 40
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Comment: C: How to retrieve sets of protein sequences?
... 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/$acc.fasta"; done > uniprot_seqs.fasta' ...
written 9 weeks ago by biohacker_tobe • 40
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Comment: C: How to retrieve sets of protein sequences?
... running this from my command line: for acc in `cat uniprot_ids.txt` ; do curl -s "https://www.uniprot.org/uniprot/$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 9 weeks ago by biohacker_tobe • 40
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Comment: C: Retrieve Protein Sequences from Uniprot
... I saw that this uses linux command directly, was curious if I could do it directly from a python command. ...
written 9 weeks ago by biohacker_tobe • 40
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Retrieve Protein Sequences from Uniprot
... 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 ...
python sequence biopython uniprot written 9 weeks ago by biohacker_tobe • 40 • updated 9 weeks ago by Shalu Jhanwar • 470
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Comment: C: get organism name from fasta file header (PYTHON)
... Thanks, this is exactly what I was looking for :D ...
written 9 weeks ago by biohacker_tobe • 40
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Comment: C: get organism name from fasta file header (PYTHON)
... Fair enough, thanks for the pointer :) ...
written 9 weeks ago by biohacker_tobe • 40
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Comment: C: get organism name from fasta file header (PYTHON)
... With linux I am aware on how to do it, but is it possible directly with python? ...
written 9 weeks ago by biohacker_tobe • 40
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get organism name from fasta file header (PYTHON)
... 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 ...
genome fasta sequence written 9 weeks ago by biohacker_tobe • 40 • updated 9 weeks ago by Joe ♦ 18k

Latest awards to biohacker_tobe

Popular Question 19 days ago, created a question with more than 1,000 views. For Co-Occurrence Network Graph & Statistics
Supporter 9 weeks ago, voted at least 25 times.
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