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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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
4k 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
60 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
29 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 ...
10 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
37 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/...
1 vote
1 answer
81 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 ...
4 votes
1 answer
70 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....
5 votes
0 answers
201 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
25 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
46 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 ...
0 votes
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5 views

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 ...
2 votes
1 answer
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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 ...
0 votes
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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 ...
2 votes
0 answers
38 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, ...
2 votes
2 answers
45 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
0 answers
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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 "...
4 votes
4 answers
160 views

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 ...
1 vote
1 answer
33 views

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&...
1 vote
1 answer
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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. ...
0 votes
1 answer
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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 ...
8 votes
3 answers
275 views

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 ...
0 votes
0 answers
27 views

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 ...
0 votes
1 answer
84 views

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 ...
0 votes
0 answers
21 views

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 ...
3 votes
1 answer
37 views

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 ...
-2 votes
1 answer
46 views

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 ...
0 votes
1 answer
20 views

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 ...
0 votes
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3 views

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?
3 votes
0 answers
32 views

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 ...
5 votes
0 answers
43 views

Gathering data on bacterial oganism growth conditions

let's say I have a list of organism names like the example below ...
1 vote
1 answer
36 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 ...
1 vote
0 answers
17 views

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 ...
0 votes
1 answer
48 views

Where did the BIND website go?

I was trying to reach the BIND (Biomolecular Interaction Network Database) but the website is down. Where can I find something similar? Has this platform moved somewhere or what?
1 vote
1 answer
62 views

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: <...
1 vote
0 answers
40 views

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 ...
1 vote
1 answer
40 views

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 ...
1 vote
0 answers
43 views

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 ...
8 votes
1 answer
590 views

Publicly available, free, complete database for antibiotics names and classes?

This is a tough one I think: is there a publicly available, up-to-date, free, complete database for antibiotics names and classes? I am specifically looking for information like, e.g., ...
6 votes
1 answer
78 views

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 ...
1 vote
1 answer
38 views

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 ...
1 vote
3 answers
759 views

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: ...
4 votes
1 answer
148 views

Is there a database of protein sequences/structure along with their melting temperature?

Such databases have been constructed for example in here or here. But I can't find them anywhere online. Can someone point me to where I can find one available online? Otherwise I'll have to write to ...
0 votes
1 answer
427 views

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 ...
3 votes
3 answers
1k 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).
1 vote
0 answers
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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 ...
15 votes
3 answers
937 views

Publicly available genome sequence database for viruses?

As a small introductory project, I want to compare genome sequences of different strains of influenza virus. What are the publicly available databases of influenza virus gene/genome sequences?
7 votes
1 answer
1k 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 vote
1 answer
404 views

What would be a reasonable healthy data set/control group to compare with a cell line from TCGA?

Assume I want to run a simple machine learning of healthy/non healthy classification, how can I use TCGA where it has only data of people with cancer. What do usually people do for example for study ...
2 votes
0 answers
118 views

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, ...