User: Jenez
Jenez • 520
- Reputation:
- 520
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- Location:
- Sweden
- Last seen:
- 3 years, 5 months ago
- Joined:
- 4 years, 11 months ago
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Posts by Jenez
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... I'm a python type of guy, and what I would do is to set up a script to [parse through the genbank file using biopython.][1]
I wouldn't expect to find any source that has any old locus names that are missing from the NCBI genbank files. Gene annotations are constantly updated and it's not unusual fo ...
written 3.5 years ago by
Jenez • 520
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... Some assemblers such as spades allows you to input what's called 'trusted contigs' which I guess might fulfil your needs? Run an assembly of the sequence reads and input your existing fasta sequence as a trusted contig. ...
written 3.7 years ago by
Jenez • 520
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... That's certainly one way of doing it. Maybe we'll see some proper integration in the future. Thanks mate. ...
written 3.7 years ago by
Jenez • 520
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... Hello biostars community,
I was wondering if anyone could point me in the right direction for searching for antibiograms for a particular species on NCBI's biosamples?
An example page can be found [here.][1]
I've so far been unable to find a way to search specifically for entries containing antib ...
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... To be honest with you GO terms and the like is not something I have a lot of expertise of. Someone can probably help you out better than I, but if you specify what exactly it is you want to achieve with the name I might be able to point you in the right direction in terms of automation. It's all a m ...
written 3.7 years ago by
Jenez • 520
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... If you go to NCBI and simply search using the term **NT01EI_0934**, you will find [this gene entry][1].
You see here that the locus tag differs from the one you have. That's because you have yielded the 'old locus tag' from the sequencing centre. Whether this makes a difference I do not know, but i ...
written 3.7 years ago by
Jenez • 520
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... I would take a guess and say that the default settings for each parameter can be found on the documentation page for [bwa mem here.][1]
See the values within [ ] for the default parameters.
[1]: http://bio-bwa.sourceforge.net/bwa.shtml ...
written 3.8 years ago by
Jenez • 520
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... What I fear might happen is as I expressed in the question; that the settings can not be tweaked enough to ensure that all 150bp regions of all genes are checked against the query's 150bp regions put in.
'Fair idea' is unfortunately not good enough in this case.
Thank you for your input ...
written 3.9 years ago by
Jenez • 520
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... You've summarized it accurately.
I did consider writing a python script for this comparison, but I fear that it will run incredibly slow. I might just time a subset and estimate how long it will run for.
Thank you for your input ...
written 3.9 years ago by
Jenez • 520
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... I have a collection of gene sequences, for each I would like to identify any highly similar 150bp regions within a specific assembled genome.
I have initially tried megablast, where I blasted each query gene against the genome and looked for regions with a sequence identity > 85%. However, it b ...
written 3.9 years ago by
Jenez • 520
Latest awards to Jenez
Scholar
3.5 years ago,
created an answer that has been accepted.
For A: How to use a fastq file from paired library layout
Student
3.6 years ago,
asked a question with at least 3 up-votes.
For Any tools available to generate fake raw reads from assembled genomes?
Teacher
4.0 years ago,
created an answer with at least 3 up-votes.
For A: Error passing generated fasta to blastn in biopython
Scholar
4.0 years ago,
created an answer that has been accepted.
For A: How to use a fastq file from paired library layout
Scholar
4.2 years ago,
created an answer that has been accepted.
For A: How to use a fastq file from paired library layout
Student
4.3 years ago,
asked a question with at least 3 up-votes.
For Any tools available to generate fake raw reads from assembled genomes?
Supporter
4.3 years ago,
voted at least 25 times.
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