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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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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SwissVar 2016 release

I am trying to find the October 2016 release of the SwissVar Database (which was discontinued since 2020). I already tried the Uniprot FTP site but was only able to find the 2021 release. Any ideas ...
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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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DAVID returning invalid KEGG pathways in gene enrichment analysis

I'm using the latest version of DAVID Knowledgebase (v2021q4, Available at https://david-d.ncifcrf.gov) for enrichment of a set of genes that I have. Using the ...
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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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Why is there a drop in the publication's rate of protein-sequences in UniProtKB/SwissProt

UniProt provides two databases 1: UniProtKB/TrEMBL (TE) with entries for which the annotations are derived from the European Nucleotide Archive. UniProtKB/SwissProt (SP) with entries for which the ...
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2 votes
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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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2 votes
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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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NMR methodology on IDP

I'm working on data that contains IDPs, the whole papers talk about NMR. So, anyone can explain the role of NMR methodology on IDP?
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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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1 answer
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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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3 answers
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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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8 votes
3 answers
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How to import large .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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6 votes
1 answer
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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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1 answer
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How to select specific lines and specific columns

Please I'm a beginner in using R and I work on database. I have a database 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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1 answer
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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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1 answer
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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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2 votes
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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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2 votes
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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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Calculating polarity and hydrophobicity of a ligand/small molecule

I have lot of SMILES IDs of the ligands. What I am interested in is the polarity and hydrophobicity score of each of the ligands. In other words, does ligand have more polar groups and can it make ...
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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-...
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2 votes
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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, ...
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1 vote
1 answer
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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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3 votes
1 answer
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How to query NCBI (Nucleotide database) by a feature qualifier?

I cannot seem to find a way to query nucleotide database (https://www.ncbi.nlm.nih.gov/nuccore) by a specific qualifier of the feature. For example, by /host under the feature "source". For example, ...
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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 ...
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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 ...
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1 vote
1 answer
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Database of RNA-Seq and SNP genotyping data

I need to obtain publicly available RNA-seq + SNP genotyping data for a cohort - ideally one where the RNA-seq data has been sequenced from brain tissue. I have found CMC and GTEx to be sufficient ...
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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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2 votes
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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 ...
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2 votes
1 answer
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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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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 ...
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Vegetable databases usage

Good morning, I'm aligning with blast some species, against all nt database to analyse the vegetables. However, in some cases we have species of animals mixed with vegetables and want only to detect ...
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-3 votes
3 answers
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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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