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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How can I resolve `bind_rows()` error?
So I wanted to download massive amounts of COX1 (or COI) sequences from any available database. I found this script in https://bioinformatics.stackexchange.com/a/13187/16657 this comment that achieves ...
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Sql query slow on Chembl postgres database
Doing complex sql query on Chembl database and it takes 40 minutes on the machine from lab.
I was thinking using dask, extract each table and export to parquet, when do the data processing .
Is this a ...
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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 ...
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Passing strings for password, email authentication and download link
Hi I am downloading the data from a website which requires authentication of email_id and password before the download. They then provide the download link which is used to download dataset. This ...
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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
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Which human reference genome version does VARAdb use?
I am interested in annotating a list of variants using VARAdb. My coordinates use the GRCh38 (hg19) reference genome. However, I do not know which coordinate system VARAdb uses.
A section of the ...
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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. ...
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How to set Entrez Direct - ESearch NCBI entrez to pipe or ignore errors?
I am using the following one-liner with NCBI entrez to query their databases from the terminal (see Entrez Direct: E-utilities on the Unix Command Line:
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Why do Illumina 850k/EPIC arrays ignore CpGs which are "GC" in the forward strand?
CpGs are symmetrical, in that a CG sequence on the forward strand is hybridized to a GC --- and both dinucleotides on each opposing strand are CpGs dinucleotides which can be methylated. Conversely, ...
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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 ...
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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 ...
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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,...
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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 ...
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postgreSQL error: "ERROR: invalid input syntax for type numeric: NULL" [closed]
I'm new to SQL. I have a table with a column of numeric type that include NULL values. I built the table structure in postgresql, when I try to import my table I get the following error:
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Where to find database for breast cancer phenotype?
Where can I find databases for breast cancer mutations (SNPs & indels) phenotype, with chromosome, position, ref, alt, gene, clinical significance.
So far, I have only found the Clinvar database.
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Database to download with information of bacteria?
I am looking for tidy tabular dataset that contains known bacteria and fungi down to the species level. Basically a table that includes genus and species names and other higher-level information. For ...
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Querying The Cancer Genome Atlas (TCGA) for gene expression
The UCI gene expression cancer RNA-Seq dataset (https://archive.ics.uci.edu/ml/datasets/gene+expression+cancer+RNA-Seq) consists of 5 types of cancers (BRCA, KIRC, LUAD, COAD, PRAD) and gene ...
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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, ...
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Is there a publication database or search engine offering geneID or UniProtID correlation?
Do we have a publication database or search engine that offers geneID or UniProtID correlation?
For example, I search "IPS cells" -> I want to know what genes or proteins are under active ...
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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 "...
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Complete List of IUPAC Chemical Naming Conventions for Formal and Trivial Names?
Two-parted question:
Where is a cheatsheet or complete list of the "formal" IUPAC naming conventions?
Where is a cheatsheet or complete list of the "trivial" or "informal&...
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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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Where can I get info about A. thaliana proteins' locations?
I have a list of A. thaliana proteins and I'd like to know their location in the cell. I've found SUBA but they seem not to share their dataset and only allow queries through their website. It's ...
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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
...
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Different structures of same protein from two softwares
I used AlphaFold and Swiss-Model to get the structure of a protein (KiSS1R) and then compare them. The structures don't match and I was wondering why the softwares produce models that are different ...
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Is there any database about the abundance of proteins in urine of healthy patients?
I have a dataset about adundance of urine proteins from cancer patients. I would like to compare these abundance levels to healthy patients' urine proteins. However I don't have any data with healthy ...
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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 ...
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Where can I find a basic example for testing association between a phenotype and each of the variants of a chromosome?
I am a statistics student trying to find data suitable for a particular method. From what I have read so far, it is of interest to determine if variants within a chromosome are associated with a ...
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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 ...
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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 ...
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How to specify the list of contigs in AGP gap file used for ENA submissions
I am battling the submission of scaffolded assembly to EBI, somehow I can not get AGP gap file right.
background
The only option seems to be using the Webin-CLI submission interface. For the ...
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Biopython BioSQL error : AttributeError: 'DBSeq' object has no attribute '_data'
Hi I am playing with Biopython and BioSQL,
I manage to create an MySQL database using Managing local biological databases with the BioSQL module tutorial:
and load 2909 fasta sequences in it through:
<...
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Question about public availability of human SNP dataset with country of origin
Is there a publicly available data set for humans SNPs, preferably together with the country of origin? If so, could someone please point me towards it.
I've looked through other questions on the site ...
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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 ...
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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 ...
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Are there any databases for gene co-expression or expression pattern clustering?
I am currently working on gene clustering based on co-expression pattern in mouse brain. The problem is I do not have some solid way to test my result. Are there any suggestions for databases ...
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Filtering Sequences (entries) by headers ID from a Fasta file database
First of all, sorry if this question has been posted previously (I could not found a solution accessing the previous Q&A).
I have a fasta file as follow:
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How to import a large amount of .bed, .gff, .vcf, .paf, .sam files into an SQL database?
Are there best practices to load different bioinformatics file formats such as VCF, BED, GFF, and SAM to SQL databases? I am wondering how people out there do that efficiently.
All of these three ...
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How to search for high coverage SRA entries
The Question
I want to find high coverage SRA entries, e.g., above 100x.
I guess the best way is to use https://www.ncbi.nlm.nih.gov/sra with an appropriate search term. I don't mind if the search ...
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How to select specific lines and specific columns
I have a data frame that contain lot of columns and lines, like this for example
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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 ...
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Is there a Python program that is able to show convergent and divergent evolution on a phylogenetic tree?
I was wondering if there was a Python program that detects convergent and divergent evolution on a tree. I am also curious if it is just better to look at a phylogenetic tree and conclude what is ...
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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 ...
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How many entries in PDB have SS bonds?
Is there a way to figure out what percentage of entries in PDB have SS bonds?
In addition, what other types of bonds in PDB may be worth looking into (not H bonds)?
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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 ...
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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.
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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/...
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