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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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Is there a way to download all data containing amino acid sequence - secondary protein structure from protein data bank

Is there a way to download all data containing amino acid sequence - secondary protein structure from protein data bank(https://www.rcsb.org/). Or is there a way to extract the data programaticaly ...
3 votes
1 answer
47 views

BLAST Database error: No alias or index file found for nucleotide database

I have created a database and added environment variables, but an "error message" still appears. How can I solve it? ...
10 votes
2 answers
1k views

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 ...
1 vote
1 answer
103 views

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,...
16 votes
3 answers
8k views

What are the advantages and disadvantages between using KEGG or Reactome?

As enrichment analysis a usual step is to infer the pathways enriched in a list of genes. However I can't find a discussion about which database is better. Two of the most popular (in my particular ...
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22 views

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 ...
1 vote
2 answers
77 views

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 ...
4 votes
2 answers
125 views

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....
6 votes
1 answer
72 views

Gathering data on bacterial organism growth conditions

let's say I have a list of organism names like the example below ...
4 votes
1 answer
44 views

SARS-CoV-2 sequence used in the AlphaSeq Antibody Datasets to predict binding affinity

Currently we are building a sequence based deep-learning model to predict binding affinity between antibody and antigen. For this we are training a sequence based model with AlphaSeq Antibody dataset (...
3 votes
2 answers
165 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 ...
-1 votes
1 answer
35 views

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 ...
2 votes
0 answers
240 views

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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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 ...
1 vote
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77 views

Need help with binding DB API

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1 vote
1 answer
255 views

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 ...
2 votes
1 answer
589 views

Python scripting with ete3 to query NCBI's Taxonomy: "sqlite3 Warning (can only execute one statement at a time)"

I am using this script: ...
2 votes
1 answer
86 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 ...
1 vote
1 answer
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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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55 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 ...
7 votes
1 answer
2k views

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 ...
-1 votes
3 answers
262 views

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 ...
3 votes
1 answer
44 views

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 ...
2 votes
0 answers
261 views

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 ...
3 votes
1 answer
63 views

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 ...
5 votes
0 answers
83 views

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). ...
1 vote
0 answers
43 views

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. ...
1 vote
1 answer
158 views

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: ...
1 vote
1 answer
59 views

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, ...
0 votes
1 answer
1k views

How to select specific lines and specific columns

I have a data frame that contain lot of columns and lines, like this for example ...
9 votes
2 answers
790 views

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 ...
5 votes
2 answers
440 views

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 ...
1 vote
0 answers
136 views

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 ...
2 votes
0 answers
43 views

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 ...
2 votes
0 answers
46 views

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 ...
2 votes
0 answers
29 views

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 ...
1 vote
0 answers
48 views

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 ...
1 vote
1 answer
161 views

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 ...
1 vote
0 answers
4k views

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: ...
1 vote
1 answer
7k 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: ...
2 votes
1 answer
231 views

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. ...
2 votes
0 answers
90 views

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 ...
11 votes
5 answers
4k views

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 ...
2 votes
0 answers
43 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 names/...
5 votes
0 answers
411 views

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 ...
1 vote
1 answer
44 views

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 ...
2 votes
1 answer
47 views

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 ...
2 votes
1 answer
152 views

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 ...
2 votes
2 answers
47 views

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 ...
1 vote
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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 "...