User: Darill

gravatar for Darill
Darill30
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6 hours ago
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1 year, 7 months ago
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Posts by Darill

<prev • 98 results • page 1 of 10 • next >
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Comment: C: Use esearch on python to get nucleotide sequence from the protein ses id
... yes it is done thank you :) ...
written 5 days ago by Darill30
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Comment: C: Use esearch on python to get nucleotide sequence from the protein ses id
... Ok thank you I tried in python : handle = Entrez.efetch(db="sequences", id="YP_001883411.1", rettype="fasta_cds_na", retmode="text") ...
written 14 days ago by Darill30
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Use esearch on python to get nucleotide sequence from the protein ses id
... I would like from a protein fasta file to get the corresponding NCBI nucleotide sequences in a new fasta file. I know that `esearch` can do it in python but I do know how to handle it with fasta file etc. I guess it should be something like: from Bio import SeqIO import Entrez wi ...
python esearch entrez written 14 days ago by Darill30
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Get pvalue and/or confidence interval of dN/dS from the codeml output
... Hello, I'm actually using the `ete3 toolkit` package from `python` in order to run the `codeml program from PAML`. So I had : -1 codon aligned sequences file -1 phylogenetic tree and I was interesting on the `dN/dS per branch` in my phylogeny, so I got the following output: branch ...
python dnds written 22 days ago by Darill30
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Recover from protein ID the corresponding nucleotide ID .
... Hello, does anyone know an automated way from an ID protein sequence to recover an ID and/or nucleotide sequence ? For exemple I have the protein ID sequence : YP_009344822.1 which is : >YP_009344822.1 transcription associated protein [Pea leaf distortion virus] MRSSSPSKDHYTQVP ...
fasta python ncbi written 28 days ago by Darill30 • updated 28 days ago by massa.kassa.sc3na160
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Comment: C: Count number of monophyletic groups within pylogeny
... Thank you ! it works like a charme :) ...
written 7 months ago by Darill30
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Count number of monophyletic groups within pylogeny
... Hello, I wondered if it whas possible within a newick tree to count the number of monophyletic groups even if intruders are splitting this group. Here is an exemple Let say you have the following three : `((A,A),((B,B),((A,A),A))));` here in that case `A` are species belonging to the `Genus A` fo ...
phylogeny monophyletic written 7 months ago by Darill30 • updated 7 months ago by Joe15k
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What kind of protein matrix substitution use for blastX divergent sequences
... I'm actually trying to find some homology between sequences inside a genome and several viral proteins in a database. As you all know, virus evolve very quickly, so I'm expecting to find a lot a divergences between the sequences I compared. In the literature I see that BLOSUM < 62 are used for ...
matrix homology diamond blast written 9 months ago by Darill30
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Comment: C: output path issue on Busco (python)
... Yep it works if I modify it directly in the config.ini file of course but the output path will change depending on the script I use... I have around 100 script to run with a unique path for each job, that is why I want to incorporate the out_path directly in my script and not in the config.ini whi ...
written 10 months ago by Darill30
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Comment: C: output path issue on Busco (python)
... Yes I removed the ; part but there is still the same issue. ...
written 10 months ago by Darill30

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