User: erica.fary
erica.fary • 0
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Posts by erica.fary
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... Sorry, my edit was not so clear... I would like to do this for all results returned by the query "ycf2[Gene Name] AND txid4097[Organism]", NC_001879.2 was just an example..
I tried also this command (ideally I would like gene sequences in fasta format) :
esearch -db nuccore -query "ycf2[Gene Name] ...
written 4.4 years ago by
erica.fary • 0
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... Hello everyone,
I encounter the following problem: I have a list of chloroplast gene IDs and a list of taxonomic IDs, and I want to retrieve for each organism all the nucleotide sequences of the gene list. This seems pretty simple: I "just" want to retrieve all sequences in fasta format. It is not ...
written 4.4 years ago by
erica.fary • 0
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... Hi everyone,
I need to build phylogenetic tree based on aligned DNA sequences. I used first from Bio.Phylo the following functions:
distM = DistanceCalculator('ident').get_distance(my_aligned_sequences)
tree = DistanceTreeConstructor().nj(distM)
However, I would like to compare the sequences u ...
written 5.3 years ago by
erica.fary • 0
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5.2 years ago by
Biostar ♦♦ 20
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... Hello everyone !
For my project, I need to import in a Python program mtDNA and Y-STR haplogroups trees like the ones available at http://www.phylotree.org/tree/main.htm and http://www.isogg.org/tree/ respectively.
Does everyone know if it is possible to extract these in newick, phyloxml, NEXUS or ...
written 5.4 years ago by
erica.fary • 0
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5.4 years ago by
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... Hi everyone,
I need to retrieve the age of the taxons that you can see when you click on the gene tree on Ensembl (e.g. here : http://www.ensembl.org/Danio_rerio/Gene/Compara_Tree?db=core;g=ENSDARG00000062209;r=17:22087864-22117363) in million of years (e.g. Bilateria 937 MYA). Has anyone an idea ...
written 5.6 years ago by
erica.fary • 0
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5.6 years ago by
abascalfederico • 1.1k
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... Hi everyone,
I need to retrieve the phyletic age (in million of years) of all the (protein-coding) genes for many organisms. I have been told that I could extract this from the Ensembl database using Perl API or MySQL query. However, I didn't find any information about how to do this (for this spec ...
written 5.6 years ago by
erica.fary • 0
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