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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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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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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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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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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Restriction enzymes with multiple recognition sequences
In a bioinformatics programming course I am currently teaching (using Python, and approached from a mostly CS rather than a biology background) I assigned a project which involves finding sites where ...
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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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Where to download JASPAR TFBS motif bed file?
I am interested in determining if any transcription factor binding site motifs are enriched in some BED files from a DNA methylation experiment.
I am looking for a database that has BED Files ...
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Is there a database of disease prevalence?
I want to collect data on how common different diseases are in different populations (or, at least, globally). Ideally, it would give me a way of querying the database with a disease name, and would ...
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Is it possible to do this in R?
I have a big clinical data file with 96 columns like age, gender, BMI, etc
I want to see which of these clinical characteristics respond to chemotherapy. Response to chemotherapy divides patients to ...
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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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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).
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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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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 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 can I work out gram staining information from the species name?
I have a very long list of prokaryote organism names. I would like to know their gram staining (gram positive or gram negative) information.
Please let me know if there is any database that keeps ...
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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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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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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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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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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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local BLAST error: BLAST Database error: Error: Not a valid version 4 database
I want to use a local blastn command to BLAST a multifasta file ~700 sequences using following command: ...
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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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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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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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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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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 ...
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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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Database with antigens and current vaccines
I am seeking virological databases focussing on:
vaccines
antibody interactions
host receptors.
Preferably the data base will host multiple strains/samples of a given virus samples.
Any assistance ...
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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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Database for proteome-wide predictions of protein structures
Accuracies of protein structure predictors have improved quite a lot in recent years. Algorithms such as Rosetta have gotten robust enough to predict structures of large number of proteins. However, I ...
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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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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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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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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 ...
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