Questions tagged [taxonomy]
Use for questions involving the assignment of a taxonomic groups to each species, the ordering of species into categories of different hierarchical value, or the classification of organisms into species, genus, family, order, class and phylum.
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How to identify a bacterium species from its short RNA-seq transcriptomics data?
I am new to RNA-seq analysis and wanted to ask if there is a method to reliably identify the species of a microbial organism using only its raw short RNA transcriptomics data. Here are some of the ...
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short Read/percentage threshold for bacterium presence in metagenome
I have ~100 paired end short read human gut metagenome samples that I classified using Kraken2. Now I want to know if a specific bacterium is in any of those samples. As far as I've searched people ...
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How many ML tree should I build?
I created a phylogenetic tree of 328 species using RAxML. I run the ML algorithm 20 times and I chose the best tree (the one with the highest likelihood).
The choice of 20 iterations was based on a ...
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tBLASTn vs NCBI TSA
Is there a way to blast my proteins against all the TSA (Transcriptome Shotgun Assembly Sequence Database) belonging to a specific taxonomy using command line?
Thanks,
Marco
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MMSeqs taxonomy running for over a day
I've been trying to run mmseqs2 on a few metagenomic assemblies and despite my best efforts in reading the wiki and playing with parameters, the process is taking over a day.
In their paper they claim ...
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getting NCBI TAXname by R
I have a data frame on R, called qIns8, with 14 columns and 204 rows. the column called "subject tax id" has NCBI taxIDs for the corresponding row, I need a script to add another column to ...
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Genetic relationships between Cyanobacteria: terrestrial vs aquatic
I believe one of the site members is an expert in Cyanobacteria hence the question.
I'm looking for a comprehensive 'phylogenetic tree' of the phylum Cyanobacteria and want to identify all the ...
M__♦
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How to add bootstrap values to the phylogenetic tree generated by OrthoFinder?
When we run the OrthoFinder analysis tool on a group of genomes to get the orthologues shared by them one of the output files include a folder named 'Species_Tree' that contains a text file named '...
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eggNOG API, how's it work?
Background eggNOG uses seed orthologues which correspond to its own internal database, so for example J421_1876 can be placed in its online search engine here. This ...
M__♦
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Parsing text within a taxonomy.csv file
I have the following file in tab separated values (TSV).
ID
Taxonomy
76980f6d906c6baaef3f96559fc7ba1b
d__Eukaryota; p__Cercozoa; c__Vampyrellidae; o__Vampyrellidae; f__Vampyrellidae; g__uncultured
...
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How can I download from NCBI all the ITS genes and the related taxonomy?
I would like to download all the ITS1 and ITS2 genes from NCBI in a fasta file. And, I'd like to download even the related taxonomy of each sequence.
Thanks,
Marco
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Assign multiple taxids to a sequence when constructing a local BLAST database
I recently had a script fail due to poor handling of BLAST output. The BLAST -outfmt staxids field usually returns a single taxid, but occasionally it returns two ...
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Mapping NCBI taxID to divergence time?
I want to map NCBI taxID, specifically a pair of Genbank sequences, to the divergence time estimate of their common ancestor. For example, using a coalescence theory approach predominantly used in ...
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List of all Latin word parts used in Biological Taxonomy?
I seem to have determined that there are 287,614 unique Latin taxonomic names used in the biological taxonomy according to the Integrated Taxonomic Information System (ITIS) taxonomy taxon.txt file. ...
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Tool that can sort NCBI taxonomy ids based on phylogeny
I have a set of NCBI txids (of varying ranks) that I want to sort in some way (e.g. a table or a tree, the way it is sorted isn't super important), based on the current NCBI data for phylogenetic ...
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Demovir produces an empty output
I am new to bioinformatics and am working on viral metagenomic (virome) datasets and so would like to use Demovir* for doing taxonomic annotations on my viral contigs.
First, I installed all ...
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Find species from FASTA files
In a school project we got the task of finding the species from two FASTA files. We got some hints of what to look for, like it is a unicellular eukaryote and that we can use blast. We don't know if ...
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Download complete Phylogenetic Tree as JSON
I would like to integrate the phylogenetic tree into a website. Does anyone know where I can download the complete tree? Best would be a JSON, which looks something like this:
...
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Comparing groups of 16S rRNA sequences - how to?
I have several groups of 16S rRNA sequences associated with taxonomic groups (let's call them A, B and C). The sequences within each group have a common ancestor and are on average more closely ...
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Software for taxonomic assignment?
I have a couple of hundred bacterial sequences of 2-30 genes of interest each, recovered from metagenomics. None of them encode rRNA. Normally I'd just BLAST the one gene I already know to be reliable ...
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Kraken2 > OTU format > Phyloseq
A collaborator has passed me over Kraken2 outputs *.report and *.kraken, from a metatranscriptomic sequencing experiment conducted on the minION.
I would like to make a tree if the data using a ...
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Generating taxonomic hierarchy by species/genus name
I am attempting to create a reference library of DNA plant barcodes in the ITS2 barcode region for plants from a specific region (Panama). I downloaded all the sequences for plants that resulted in a ...
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Determine if an organism is microbic or unicellular
I am doing some metagenomic analysis of samples which can only contain microbes due to the experimental setup.
For this, it would be useful to be able to distinguish whether a specific organism is a ...
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Analyzing a blast result of NGS data
I am analyzing BLAST results from total RNA NGS, pair ends. This BLAST results was performed against the ssRNA virus database download from NCBI.
I filtered those read data whose paired ends ...
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What is a proper way for random subsampling of metagenomic data?
Let's say we have a metagenomic sample that is paired-end FASTQ files including 10,000,000 DNA reads collected using shotgun sequencing.
How would one make a random subsample of the mentioned ...
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Which taxonomy data type to use for abundance graphs and statistical analyses?
At our institution we have had some debate about this topic. So let me give some background:
Qiime2 produces a OTU table which shows the number of sequences that matched to a specific OTU. It also ...
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Python module for fetching NCBI id for a list of species
I have a list of scientific names of species. Is there a python module that can fetch NCBI taxonomy IDs?
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157
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How to apply RDP, Greengenes and other special taxonomies in Krona?
I used Kraken 2 to classify my 16S metagenomic data using both RDP and Greengenes database. As these are special databases the taxonomic ids assigned do not match with the NCBI taxonomic ids. I found ...
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Looking for a taxonomic dataset that links tree genera (or species) to families
I am looking for a taxonomic dataset that would allow me to links tree genera (or species) to families. In particular, I am interested in the tropical species found in the Amazon.
I found a long but ...
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Python scripting with ete3 to query NCBI's Taxonomy: "sqlite3 Warning (can only execute one statement at a time)"
I am using this script:
...
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In calculating the retention index, why do we use the character state with the lowest frequency?
To calculate the retention index for a phylogenetic tree, we use the following formula:
$$\frac{\text{maximum number of steps on tree - number of steps on the tree}}
{\text{maximum number of steps on ...
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Are these standard species abbreviations and how to look up others?
Reactome uses a three letter code for each species which are listed below.
Are the letter codes used by Reactome a standard?
If so is there a web page or download file that can validate the code and ...
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Using a Bash Script to search TaxIDs against NCBI's Taxonomy yields "400 Bad Request" error?
I've been searching TaxIDs against NCBI's Taxonomy DB to get taxonomic lineages for species. I have successfully done this for 1,000's of TaxIDs that were returned to me by Blast+ blasts in a CSV. (...
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What is the difference between the entity_src_genCategory tag and the entity_src_natCategory tag in pdb-xmls?
I want to read out the taxonomy id of the source organism of a pdb entry using the xml-file of the entry that is provided under ...
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Microbial diversity analysis using whole-genome metagenomic data
I have data, obtained from a single metagenomic DNA sample, that consists of two MiSeq FASTQ files (R1 and R2) that I merged using PEAR.
Now I want to estimate the abundances of the bacteria taxa to ...
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How to convert species names into common names?
I’m trying to find common names from a list of scientific names (not all will have them though).
I was attempting to use taxize in R but it aborts if it doesn’t ...
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