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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25 views

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 ...
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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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Global SNP frequency database?

Is 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. e.g. On average, which country ...
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427 views

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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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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Meaning of the Flags attribute returned by Entrez.esummary(db='nuccore')

My Question Calling Entrez.esummary for the nuccore db returns records with various fields. One of these fields is Flags. I ...
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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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Why is the output from the online DISOPRED portal and a local DISOPRED installation different?

I recently installed DISOPRED on a computer cluster to predict the intrinsic disorder in long (~800 residues) amino acid sequences. I followed instructions provided on an online blog, since I couldn't ...
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34 views

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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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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How to compute module completion ratio of KEGG modules from KO identifiers? (command line)

I was previously using KEGG-MAPLE to compute module completion ratios for metagenome assembled genomes. However, this tool was web only (very frustrating) and also it has been discontinued. Now I'm ...
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Does stringDB R package require to be loaded before using it? [closed]

I am working with the package STRINGdb in R and this is the piece of code which has issues: ...
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1answer
30 views

Database with antigens and current vaccines

I am seeking a virological database comprising the following information: vaccine. antibody receptor. Preferably hosting multiple strains/samples of a given virus samples of strain. 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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How can I open the 16S_silva.installation.sh in kraken2?

I installed kraken2, which includes the 16S silva database. Indeed I see 16S_silva_installation.sh. How ca I install it?
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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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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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2answers
69 views

Difference between clinical significance and statistical significance

I am working on a clinical data analysis project and am from IT domain. While I am analyzing the data, I came to know that though some of the variables are not statistically significant, they are ...
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1answer
42 views

Use of Electronic Phenotype in EHR

May I know what's the use of Electronic Phenotyping using EHR data? I did refer this link but have few questions I understand that ...
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12 views

Search for XL-MS datasets

I am looking for human cross-linking mass spec datasets, where the exact residues that were crosslinked are stated. Any format, say csv, ...
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1answer
49 views

How to extract hypervariable region of mitochondrial dna from its fasta file?

Recently I've done some analysis on human mitochondrial DNA and now I want to run the same analysis on only hypervariable regions of mitochondrial DNA to see whether the changes that I have observed ...
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1answer
65 views

Are there genomics databases for neurological and psychiatric disorders?

Are there databases that relate genetic disorders with neurological disorders? I am thinking of something like COSMICS for cancer? AFAIK cancer usually develops due to a combination of 5-10 ...
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Extract sequence from nucleotide databse

Can someone tell the way to extract the fasta sequences of gene Cytb? Can I extract them in the nucleotide database? For instance, I'm trying to fetch the fasta data of Acetes japonicus of cytb gene. ...
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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 ...
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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 ...
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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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1answer
51 views

Are there databases to annotate non-coding mutations?

I would like to ask if there are some known databases that allows to annotate non-coding mutations in a given region for the human genome? Preferably, if the database is downloadable so I am able to ...
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3answers
96 views

How to obtain the standard gene name

I have a list of genes and proteins extracted from literature. How can I convert them into standard gene names.
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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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Where to find secondary metabolites in lichen (and herbal medicine)? [closed]

I've searched around and found about 80 specific secondary metabolites for lichen, but I can't seem to find anymore. They were mostly from research papers. I read that there are more than 800 ...
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1answer
23 views

Store and search on variant and annotation data

I need to store a large number of variants with their annotations. I need to import dbSNP, as well as Clinvar, and ExAC etc. Also I have sample variant data from patients. I need to be able to search ...
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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 ...
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Merging transcriptomes coming from different experiments

I'm planning to build a transcriptome by pooling all existing transcriptomes in SRA for a non-model species (which has no reference genome) to study differentially expressed genes and the like. It ...
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1answer
51 views

Find similar proteins with similar tertiary structure?

I'm a mathematician studying knotted curves and am trying to find some applications of my work in proteins. Using https://www.rcsb.org/, how do I find proteins that have similar (but perhaps not the ...
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121 views

Old versions of the reference genome and dbSNP

For benchmark purposes I’m trying to find an old version of the human reference genome (pre-GRCh37) and a matching version of dbSNP. Unfortunately it appears as though older versions of dbSNP aren’t ...
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1answer
49 views

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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How to use analysis output in my pipeline

I am running an analysis and I want to edit the output that I received from that analysis. However I cannot define the output name in my pipeline, because after running the analysis it is asking me to ...
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2answers
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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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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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ANY (technical) reason behind submitting sequences to GenBank versus ENA Sequence

The DNA sequence sections of the three INSDC databases (i.e., DDBJ, ENA Sequence and GenBank) are synchronized periodically and strive to keep their stored data as ubiquitously accessible as possible. ...
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List of human transcription factors

I'm looking for a list of human transcription factor (TF) genes. Where can I find a TF database or how can I retrieve this list from other databases?
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Where can I find hemagglutination inhibition (HI) assay data?

I am looking for hemagglutination inhibition assay data for type A influenza virus. Could someone please give me a link to a database with this information? Thanks.
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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 ...
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792 views

Receptor-ligand database

How can I find ligands of receptors (or vice versa)? For example, I want to find the receptors of IL-8 (CXCL8).
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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 ...
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Gathering data on bacterial oganism growth conditions

let's say I have a list of organism names like the example below ...