User: john

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john70
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Posts by john

<prev • 29 results • page 1 of 3 • next >
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tblastn cuts querry even when alligment cut be better if extended
... I am trying to blast proteins on a single genome. So I build a nucleotid database of the genome and used tblastn to align the query proteins on the genome. I did not change any standard parameters. tblastn -query protein.fasta -db genome.fasta The protein.fasta file looks like this: > ...
ncbi tblastn blast written 3 months ago by john70 • updated 9 weeks ago by lieven.sterck3.3k
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Comment: C: Error with biopython pairwise aligner
... it has not the same functionality ...
written 4 months ago by john70
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Error with biopython pairwise aligner
... I try to use the pairwise aligner provided by biopython. But I fail to get the examples working. When I execute the following code: >>> from Bio import Align >>> aligner = Align.PairwiseAligner() The second lines returns the error: Traceback (most recent call last): ...
biopython written 4 months ago by john70
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Comment: C: Retrieve reference genome for a taxonomic id from NCBI automaticaly
... Not if you checked the sixth column for txid there it is either "reference genome" or "representative genome". At least in the current version. I think it will be different if you use the seventh column (txid of the specie). I think that is why they have the term "reference genome" and "representati ...
written 8 months ago by john70
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Comment: C: Retrieve reference genome for a taxonomic id from NCBI automaticaly
... I think I will simply try reference genome and representative genome. Like so: #!/bin/bash TAXID="$1" if [[ -z "$TAXID" ]]; then echo "Usage: retrieveReference.sh NcbiTaxId" exit else if [[ ! -e assembly_summary_genbank.txt ]]; then wget ftp://ftp ...
written 8 months ago by john70
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Comment: C: Retrieve reference genome for a taxonomic id from NCBI automaticaly
... Hey nice job. Almost perfect, the script just fails in a few cases when there is no good assembly so NCBI did not give it the status as a official reference genome. In this case they seem to provide the last assembly in the genome db. So I extend your script to do that. #!/bin/bash TAXID="$ ...
written 8 months ago by john70
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Comment: C: Retrieve reference genome for a taxonomic id from NCBI automaticaly
... But they do it! They provide a reference genome per taxid! I showed that in the question! You simply take the URL https://www.ncbi.nlm.nih.gov/genome/?term=txidFOOBAR[Organism:exp] Than go one the right side to genome. Hit the link in the first line: Reference genome: FOOBAR And voila you are t ...
written 8 months ago by john70
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Comment: C: Retrieve reference genome for a taxonomic id from NCBI automaticaly
... Hm maybe I should clarify my problem a bit. I have a list of txid and I want to download for each one of them 1 genome. The list is to big to do it by hand and also might change and must be redone. Hence I want to make it automatically. I dont want to decide which genome to take if there a multiple ...
written 8 months ago by john70
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Comment: C: Retrieve reference genome for a taxonomic id from NCBI automaticaly
... Probably there is a reason that NCBI is what it is and much like in biology just makes sense in the light of history/ evolution. But still NCBI made the effort to provide the public for every txid of a species or strain (and I don't want to go into the discussion what these two terms mean. For me i ...
written 8 months ago by john70
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Comment: C: Retrieve reference genome for a taxonomic id from NCBI automaticaly
... Uh NCBI is a mess. "Best" is the wrong word, but there is an "official" one. At least one genome is linked with the taxid by the way I described. But this is also probably a little arbitrary and nobody is really checking which assembly should be the representative for the specie. With the way you sh ...
written 8 months ago by john70

Latest awards to john

Student 8 months ago, asked a question with at least 3 up-votes. For Retrieve all sequence ids from a master record
Popular Question 3.0 years ago, created a question with more than 1,000 views. For blast error invalid query/ sequence/ filtering options. What is the problem?

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