User: manaswwm

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manaswwm30
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1 year ago
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Posts by manaswwm

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Bioinformatics vs. the Climate Crisis
... I think I read about a project last year in Netherlands where they were trying to build a functioning cell in silico. Maybe by UniGroningen? If anyone has any links for this please do post. That is already something in that direction. ...
written 2 days ago by manaswwm30
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Answer: A: Duplicated CDS start/stop entries in GFF-file
... @Juke-34 - Many thanks for your suggestion. However, I figured a way out to overcome this problem using the following link (*https://libraries.io/github/YeoLab/gffutils*, scroll to "Longest protein for this gene") and some addition of code. In my opinion, following should do the trick - transcr ...
written 5 days ago by manaswwm30
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Comment: C: Duplicated CDS start/stop entries in GFF-file
... @Juke-34 many thanks! I guess this should help. Just out of curiosity - I see this package is for Perl? Do you have any suggestions for python? I could always just trim the file of the short isoforms (thanks for correcting me) and load it in python (I suppose?) and then perform the next tasks, but ...
written 8 days ago by manaswwm30
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Duplicated CDS start/stop entries in GFF-file
... Hello, I am trying to extract information from a gff-file using the *gffutils* package (https://daler.github.io/gffutils/) in python. After creating and loading the "local database" from the gff-file, I want to extract CDS entries for every gene entry (start and stop positions of the CDS), however, ...
gff-file python gffutils written 8 days ago by manaswwm30
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Comment: C: How to get fasta sequences of features from a GFF3 file?
... Biopython? They have plethora of methods mimicking the central dogma essentially ...
written 29 days ago by manaswwm30
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Answer: C: network visualization (multiple data source integration)
... Of the tools that I have used so far: -Gephi in my opinion has better layouts and visualization for large networks (compared to cytoscape) -GeneMania (available in cytoscape or as an independent tool on internet) has better visualization features for regular sized networks ...
written 9 months ago by manaswwm30
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Comment: C: Two bioinformatician positions
... Interested in the positions (if they are still available). How do I make an application? ...
written 12 months ago by manaswwm30

Latest awards to manaswwm

Teacher 8 months ago, created an answer with at least 3 up-votes. For C: network visualization (multiple data source integration)

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