User: Hugues

gravatar for Hugues
Hugues250
Reputation:
250
Status:
Trusted
Location:
Oslo, Norway
Last seen:
2 years, 2 months ago
Joined:
5 years ago
Email:
h****************@gmail.com

Posts by Hugues

<prev • 30 results • page 1 of 3 • next >
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Answer: A: Mapping Refseq Ng_ Regions To Chromosome Position
... This has bugged me for a long time! Thanks @nmb for asking and @deanna.church for answering. Now that you have the GFF3 file on disk, you can $ cat GCF_000001405.25_refseqgene_alignments.gff3 | grep NG_017013.2 | cut -f1 -f4 -f5 NC_000017.10 7563097 7595868 to get the chromosome, start and ...
written 4.5 years ago by Hugues250
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Comment: C: Consensus sequence software?
... Wow! What an exhaustive research!!! Wouldn't it have been just faster to code it yourself? I compute the consensus sequence from the Position-Weight Matrices (PWM). Biopython can do it (yes I know you don't want it -that'a why it's a comment and not an answer). ...
written 4.9 years ago by Hugues250
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Comment: C: Modify location of a GenBank feature
... Thanks for posting your code / solution, I'm sure it can help others. ...
written 4.9 years ago by Hugues250
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Comment: C: blast against genomes in biopython
... There is no alignment. ...
written 4.9 years ago by Hugues250
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Comment: C: Is it possible to download a random set of proteins? (fasta files)
... You should edit your question, add something like Edit 1 at the end of it with your progress. Not as an answer (?) Or post a new question if really that doesn't work. ...
written 4.9 years ago by Hugues250
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Comment: C: How to retrieve nearest genes in Ciona genome?
... You could create a new question: how to map VISTA coordinates to NCBI (ciona)? and cross-ref it here. I don't know how to tackle that though, but I'd be interested to learn about what you find out. ...
written 4.9 years ago by Hugues250
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Comment: C: Modify location of a GenBank feature
... Show me some love. Vote me up! I'm paid in rep. points :-) ...
written 4.9 years ago by Hugues250
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Comment: C: Modify location of a GenBank feature
... "how to modify the locations" -> I've answered in my Edit 1. Please try it out and let me know. "while importing the features into a new GB file" -> I haven't tried hard yet. Have a go at it yourself. Edit your question where you show us your attempts. ...
written 4.9 years ago by Hugues250
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Answer: A: Modify location of a GenBank feature
... Where is the question? Do you get an error message? Well I do get one: when I do something like: features.location.start.position = newstart I get an error: seqfeature AttributeError can't set attribute And it doesn't matter whether the genbank file was open read-only as you did, or in writing ...
written 4.9 years ago by Hugues250
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Comment: C: Modify location of a GenBank feature
... Cross-post from http://stackoverflow.com/questions/24636588/modify-location-of-a-genbank-feature I guess that you didn't get an answer there. But the link and explanations over there can be useful. ...
written 4.9 years ago by Hugues250

Latest awards to Hugues

Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: Is it possible to download a random set of proteins? (fasta files)
Scholar 4.9 years ago, created an answer that has been accepted. For A: Question about strand orientation.
Scholar 4.9 years ago, created an answer that has been accepted. For A: Is it possible to download a random set of proteins? (fasta files)
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: Is it possible to download a random set of proteins? (fasta files)
Scholar 4.9 years ago, created an answer that has been accepted. For A: Question about strand orientation.
Supporter 4.9 years ago, voted at least 25 times.
Commentator 4.9 years ago, created a comment with at least 3 up-votes. For C: First Intron extraction from ensembl

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