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Questions tagged [database]

A repository for data that is organised according to specific rules. Important biological databases include PDB (Protein Data Bank), Ensembl, Uniprot.

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What exactly does each of InterPro, PANTHER, Pfam bring to the table individually in classifying a protein?

I would be very grateful if somebody could sketch out the methods Pfam and PANTHER use to assign a family to a given protein and how they are different. My (cursory) understanding is that InterpProp ...
rtviii's user avatar
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Database of Cell Volumes by Cell Ontology?

Are there any databases that have aggregated information on cell volumes? Most useful would be a database keyed by cell ontology (e.g., CL:0000236 for B cell). ...
merv's user avatar
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4 votes
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Extracting a cytochrome B sequence from NCBI's nucleotide database

Can someone tell the way to extract the fasta sequences for the gene cytb of Acetes japonicus (shrimp important to China and South Korea)? Can I extract them directly from NCBI nucleotide database (i....
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Can second search with limited search space improve result in MS proteomics data?

First, please know that I am a novice in this field and that it is thus very likely that you will regard this question as basic or flat stupid. Please be gentle and don't be afraid to criticize. I am ...
Max Jonatan Karlsson's user avatar
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PROKKA setupdb / cmpress error

I am trying to run --setupdb in Prokka, but I'm getting this error that I can't seem to find the answer for. When I run prokka --setupdb I get ...
Carol Luz's user avatar
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What codes represent what genes?

I want to run experiments on the data used in PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF link So far, the paper has reduced the dimension to ammon's ...
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How does one convert "flowJO" flow-cytometry cell-count, etc, bead, etc data into .json or relational-database-management-system compatible files?

How does one convert "flowJO" flow-cytometry cell-count data into ".json" or relational-database-management-system compatible files? The way flow-jo exports is in wide rather than ...
Coo's user avatar
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Building database for MetaCache takes extremely long

A question to those who have experience with MetaCache (metagenomic tool): I have tried to build the MetaCache taxonomy from refseq (only bacteria), as described in the EXAMPLES here. However, the ...
Roger V.'s user avatar
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What is the difference between flat and stereo stitch id?

For my thesis, I'm working on side effect prediction in a machine learning framework and I am working on data available on SIDER (http://sideeffects.embl.de/download/). If you open the README file, ...
Elisa's user avatar
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Mapping ICD9 codes in UKBB data to PheCodes using PheWAS package

I am working on the UKBB data and trying to specify cases and controls by converting ICD9 codes to PheCodes. I have input data (icdt) where the first column (f.eid) is patient IDs and the remaining ...
Muhammad's user avatar
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Finding original papers for gene annotations

I am wondering if there's a database to look up the annotation history of an arbitrary gene/ORF, with links to the primary literature for each step of the annotation. I have found that neither NCBI ...
biohacker's user avatar
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Grabbing all Immune related genes with databases in R

I am having trouble grabbing specific pathway info using databases in R. I have RNAseq results and I want to remove immune related genes from the current list that I have. With a vector of gene names/...
James's user avatar
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Global SNP frequency database?

Is NCBI's dbSNP the most comprehensive database of SNP frequency? I'd like to get the largest possible database of allele frequencies per 'population' or geographic region. For example, on average, ...
Dan Bolser's user avatar
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741 views

Cannot blast against specific NCBI databases

I am having issues with some prokaryote reference genome databases (exact names : ref_prok_rep_genomes.*), that I downloaded from the NCBI website : https://ftp.ncbi.nlm.nih.gov/blast/db/. Files in ...
Olivier Coen's user avatar
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144 views

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 ...
Ahmed Abdullah's user avatar
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Does anyone have older versions of NT and 16s RNA DB from NCBI?

I am in search of past years' versions of NT and 16s databases from NCBI. I recently contacted NCBI about this and they replied: Unfortunately, we do not archive past versions of the blast ...
ljs's user avatar
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Need help with binding DB API

...
Neeleshwar Pandey's user avatar
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Download Addgene database

Is anyone aware of a way to download all vector sequences from addgene at once? As a non-profit, I'd assume they shouldn't be opposed to making this data available, but it doesn't seem to be possible. ...
Anonymous's user avatar
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1 answer
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Lower case vs. upper case nucleotids in sequence vs. dots at the end

What is the difference between lower case and upper case nucleotides in a sequence? My other question is what are the dots at the end of the sequence? Some examples are shown below: GGgG,GGgG,GGgG,...
David Khutsishvili's user avatar
1 vote
0 answers
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GSEA. Subsetting Gene Ontology, Biological Processes, by gene set families of interest

I have run GSEA - on Gene Ontology , Biological Processes (GO and BP hereafter) - on some Mouse bulk RNA-seq data, and am currently in the process of going through the results. To do this, I have used ...
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Production database system for storing vcf records

I’m standing up a production bioinformatics pipeline that’ll be producing standard VCF files. I’d like to store this data in an SQL database that ingest the VCFs and allow me and my team to easily ...
Jessime Kirk's user avatar
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How to get a list of all human morphogens?

Gene Ontology provides many genes annotated as taking part in various morphogenesis processes but I want to get a list of all morphogen coding genes specifically. Uniprot does not have "...
Sashko Lykhenko's user avatar
1 vote
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24 views

How to interpret complete genome sequence in NCBI

I have a very basic and quick question: does the complete sequence of nucleotides of an organism (for example this one that I am considering in my homework of Pyrococcus Fuoriosus) reported in NCBI ...
HelpNeederStudent's user avatar
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Which database is good to store (metagenomic) relative abundance data?

The simple question is: how to store relative abundance data in a database? Which database to choose? I am talking here about metagenomics data, relative abundance of species or some features. Each ...
Art's user avatar
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Error during File conversion

Conversion of a multi-entry sdf to a multi-entry pdb file with open babel results in the loss of the compound names in the resulting PDB file. Why do you think this might occur and how can I resolve ...
ibio_rep1's user avatar
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151 views

How to deal with the mismatches between gene names obtained from different sources?

For most of the time, I rely on gene ids to combine different datasets. However, in some instances, I have to combine datasets based on gene names. Then, if I don't know the source of gene names in ...
user345394's user avatar
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1k views

Parse Error while using AutoDock Vina

I am trying to dock ligands with proteins to estimate the docking potential however, I am facing this error while docking. Any help will be highly appreciated.
ibio_rep1's user avatar
1 vote
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25 views

How do protein-protein interaction databases work?

I am a student and just trying to gain a base level understanding of PPI databases and how to interpret their data. For example, when inputing multiple genes into String, does it only give protein-...
DN1's user avatar
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How to (efficiently) search nuccore to retrieve only annotated sequences?

I wish to efficiently search nuccore to retrieve only annotated sequences. By "annotated" I mean that the nuccore entry contains annotation information. An equivalent definition (if I understand ...
Oren Milman's user avatar
1 vote
0 answers
76 views

Is there a built-in parser for the textual feature table that Entrez.efetch returns?

Entrez.efetch helpfully gives me the feature table of a nuccore entry. If I understand correctly, efetch can only return the ...
Oren Milman's user avatar
1 vote
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162 views

Scientific names of taxids with kraken 2.0.8 beta, command kraken2 --use-names error

I am running kraken 2.0.8 beta to do taxonomic classification of micorbiota data coming from a MinION run based on the 16S gene. To do so I am using the pre-bult kraken SILVA database. I managed to ...
Irma's user avatar
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Calculate the percentage of the genome that is represented by some sequences

I have construct a repeat libraries using de-novo identification methods. All results from different tools has been combined into one fasta file. How can I get the percentage of how much these ...
M.Bioinfo's user avatar
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Need help in identifying origin of variants in CIVIC

We usually denote the origin of a mutation as either somatic or germline. This information is usually available in certain databases such as CIVIC, ClinVar, COSMIC etc. But when we come to variants ...
Aishwarya Parasuram's user avatar
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0 answers
39 views

Why is Clostridium difficile toxin A + B outdated in snomed?

I'm looking at the new version of the Snomed dictionary and the concept 707993000 Clostridium difficile toxin A + B (substance) is deactivated (and outdated) since ...
dedek's user avatar
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ZINC15 database: proxy server error when trying to download catalog in any format

I am a complete beginner in the use of such databases. When navigating to the ZINC15 database website and trying to download an entire catalog with the "Download all as" option the request ...
Zea Mays's user avatar
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0 answers
15 views

Uploading manifest from CCDI to CGC project

Thank you in advance for your help! I am trying to download data from the CCDI (Children Cancer Data Initiative) and I have a manifest csv file that I downloaded from the CCDI. I'm trying to upload ...
msun5040's user avatar
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54 views

Good practices for doing sanity checks when parsing multiple PDB files

This is my first time posting to stack exchange, as well as to using data-driven approaches, so please correct me if my questions is not clear enough. I am trying to parse 200+ .pdb files to extract ...
Priyanshu Gupta's user avatar
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117 views

uploading reads to ENA using aspera

Once again, I am trying to upload reads to ENA using aspera. Following their instructions I used several times in past (successfully) to upload my reads ...
Kamil S Jaron's user avatar
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0 answers
39 views

Please help me with my command!

I am looking for a command to count the total number of unique proteins in a file. For instance I wrote a command to BLAST XYZ proteins as query against the DLY proteins as a database to determine the ...
AlphaQueUp's user avatar
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39 views

Blood analysis devices: how and where is the data saved

I've read that there are blood analysis devices that can automatically determine the data for each specified analyse. You can expect to get the results in less than a day. Q: How and where do they ...
user avatar
-1 votes
1 answer
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Where can you download functional domain labels of the human genome?

I'm visualizing where mutations occur in a gene, and would like to add functional domains to the plots. I have some trouble locating sources to download data on functional domains. The dataset should ...
Sofie's user avatar
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-1 votes
1 answer
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A database for RefSeq protein accession IDs

Are there any databases or tools that contain a list of all RefSeq protein IDs for the interest organism/microorganism, e.g. get a specific microorganism name and return all RefSeq Protein IDs that ...
Ehsan Salehabadi's user avatar