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 5 months ago by john70 • updated 4 months ago by lieven.sterck3.9k
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Comment: C: Error with biopython pairwise aligner
... it has not the same functionality ...
written 6 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 6 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 11 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 11 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 11 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 11 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 11 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 11 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 11 months ago by john70

Latest awards to john

Student 11 months ago, asked a question with at least 3 up-votes. For Retrieve all sequence ids from a master record
Popular Question 3.2 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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