User: zoe.meziere

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Posts by zoe.meziere

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How to generate a family level phylogeny?
... Hi all, I want to generate a 16S family level phylogenetic tree of a bacteria family, and include on the sequence I have to see where it falls within the family. I know the SILVA database has a lot of 16S sequences, that I downloaded. But making a tree out of all those sequences requires much space ...
phylogeny 16s written 28 days ago by zoe.meziere0
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Comment: A: Generating tree from Amphora2 for Synergytwo
... Did you find a way to make a tree out the the table? I'm having the same issue. Thanks! ...
written 11 weeks ago by zoe.meziere0
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Comment: C: Metabolic pathways from list of protein ID numbers
... I actually managed to get the Uniprot IDs but I can't retrieve the KEGG IDs. I tried both the Uniprot and the KEGG tools... do you know why it doesn't work? ...
written 3 months ago by zoe.meziere0
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Comment: C: Metabolic pathways from list of protein ID numbers
... Yes sure, here are a few examples: OFW53612.1 WP_090599220.1 OGD16911.1 OGD16900.1 PKP54795.1 PKP54793.1 WP_090721821.1 PKP58768.1 PKP59194.1 OGD17541.1 This is EMBL/GenBank/DDBJ CDS identifiers ...
written 3 months ago by zoe.meziere0
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Comment: A: Metabolic pathways from list of protein ID numbers
... Thanks! I'm having trouble converting my protein IDs into KEGG IDs... They are NCBI IDs, but that database is not in the conversion tool of UniProt... ...
written 3 months ago by zoe.meziere0
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Metabolic pathways from list of protein ID numbers
... Hello, I have a list of protein ID numbers of a clade of Bacteria (obtained from metagenome), and I am trying to uncover the metabolism of that clade: hererotrophic or not, what pathways are used, presence/absence of respiration/fermentation etc. How can I do that? Is there an online tool or softwa ...
pathways protein written 3 months ago by zoe.meziere0
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Sequences of 1 marker in all Bacteria phylum
... Hi all, I am trying to make a tree of all bacterial phyla with one marker (rplc), to see where my set of protein sequences fall. Where can I find those sequences? I've been trying to use AMPHORA but can not make it work (I posted about that earlier). So I used the online tool to find the markers (t ...
phylogeny marker sequence amphora written 3 months ago by zoe.meziere0
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Can't locate Bio/SeqIO.pm
... Hi everyone, I'm totally new in programming, and I'm just trying to use Phyla_AMPHORA to get sequences of a specific marker, for all bacterial phyla to make a phylogenetic tree. But after installing so many things, including Perlbrew and Bio Perl, I now get this message while trying to run the tes ...
perl amphora written 3 months ago by zoe.meziere0 • updated 3 months ago by finswimmer9.8k

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