User: Nicojo

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Nicojo1.1k
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New User
Location:
Kyoto, Japan
Last seen:
4 years, 8 months ago
Joined:
7 years, 11 months ago
Email:
n*******@yahoo.com

I'm Nicolas Joannin, working on the varDB project at Kyoto University, Japan. Antigenic variation is a mechanism that many pathogens have found to avoid their hosts' immune system. varDB is a database of antigenic variation sequences. I come from the wet lab, but have recently shifted to working in the dry... Mostly learning Python 3.x, although I sometimes have to deal with both Perl (who doesn't ;) and Ruby.

Posts by Nicojo

<prev • 94 results • page 1 of 10 • next >
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Comment: C: Does Anyone Know About A Biopython Package For Use With The Chado Db Schema?
... Thanks for the link! And to answer your question, yes, I am interested in working on this. The only problem is that I am a beginner at programming (mostly did wet lab before), and I'm working with Python 3.x, which might be another limitation. In any case, I'll look into Jose's project, and eventual ...
written 5.0 years ago by Nicojo1.1k
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Comment: C: Does Anyone Know About A Biopython Package For Use With The Chado Db Schema?
... Thanks! I didn't pay much attention to the ChadoDjangoHOWTO because I don't know much about Django, and I thought it would only be useful for a webapp front for a DB. But I think I check now to see how it can be useful for my purposes... The Github link, as well as searches in Sourceforge and Google ...
written 5.0 years ago by Nicojo1.1k
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Does Anyone Know About A Biopython Package For Use With The Chado Db Schema?
... I am interested in using the Chado schema, which is actively developed and community supported, but it uses a BioPerl interface. I would rather use BioPython. Does anyone know of an active dev project or completed package for this? ...
biopython written 5.0 years ago by Nicojo1.1k • updated 5.0 years ago by Peter5.6k
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Comment: C: How To Retrieve All Sequences, From Ncbi, That Belong To A Specific Txid And Its
... Sorry to all: my question was initially badly worded. ...
written 5.1 years ago by Nicojo1.1k
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Comment: C: How To Retrieve All Sequences, From Ncbi, That Belong To A Specific Txid And Its
... @Neilfws, I'm sorry but your reply is not an answer to my question; I think it would have been better as a comment. I am realizing now that my question was very badly written. Sorry for that. To answer your comments, first of all, yes, I have read the documentation. Second, the example code you poin ...
written 5.1 years ago by Nicojo1.1k
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Answer: A: How To Retrieve All Sequences, From Ncbi, That Belong To A Specific Txid And Its
... Thanks to Adam's suggestion, I have found a way to do this. It seems that I can use 4 different "term" expressions in my esearch query: term=txid5833 will result in just retrieving sequences with this txid. term=txid5833[Organism] will return all the sequences with this txid, and all its sub-txids ...
written 5.1 years ago by Nicojo1.1k
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Comment: C: How To Retrieve All Sequences, From Ncbi, That Belong To A Specific Txid And Its
... @Andrzej (sorry for the name mix up), your link did help me find the answer, so thanks again for contributing in a constructive manner! ...
written 5.1 years ago by Nicojo1.1k
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Comment: C: How To Retrieve All Sequences, From Ncbi, That Belong To A Specific Txid And Its
... Thanks for the answer, unfortunately I wasn't precise enough in my question (I edited it now). I would like to know how to do so with eutils... ...
written 5.1 years ago by Nicojo1.1k
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How To Retrieve All Sequences, From Ncbi, That Belong To A Specific Txid And Its Sub Txids?
... I am trying to retrieve all the nucleotide sequences from Genbank that belong to a txid and its "children" txids, e.g. txid5833. As you can see, there are many txids under this one... I am using eutils for this, but I can't figure out how to make it retrieve search for all the sequences, including ...
genbank written 5.1 years ago by Nicojo1.1k
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Answer: A: Obtaining A Maximum Number Of Blast Hits: Problem...
... NOTE: This question and answer concerns BLAST 2.2.25+... I do not know if any of this is valid for other versions of BLAST. Answer to question #2: My initial (main) problem was that the following blast+ command... tblastn -query protein.fasta -db nucl.blastdb -out results.tblastnout -evalue 1 -ou ...
written 5.3 years ago by Nicojo1.1k

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