Skip to main content

Questions tagged [database]

A repository for data that is organised according to specific rules. Important biological databases include PDB (Protein Data Bank), Ensembl, Uniprot.

Filter by
Sorted by
Tagged with
0 votes
0 answers
19 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 ...
Zea Mays's user avatar
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 (...
Krishna's user avatar
  • 43
-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 ...
Sofie's user avatar
  • 1
0 votes
0 answers
15 views

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 ...
msun5040's user avatar
1 vote
0 answers
69 views

Need help with binding DB API

...
Neeleshwar Pandey's user avatar
1 vote
1 answer
208 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 ...
Nickmofoe's user avatar
  • 339
1 vote
1 answer
40 views

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 ...
Jack2501's user avatar
0 votes
0 answers
54 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 ...
Priyanshu Gupta's user avatar
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 ...
Priya's user avatar
  • 351
2 votes
0 answers
251 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 ...
Carol Luz's user avatar
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 ...
Cristian Riccio's user avatar
1 vote
0 answers
42 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. ...
Anonymous's user avatar
  • 111
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: ...
Sudoh's user avatar
  • 217
1 vote
1 answer
58 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, ...
ning's user avatar
  • 141
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 ...
A.Dumas's user avatar
  • 497
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 ...
Coo's user avatar
  • 131
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 ...
Roger V.'s user avatar
  • 381
1 vote
1 answer
100 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,...
David Khutsishvili's user avatar
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 ...
h3ab74's user avatar
  • 846
1 vote
0 answers
131 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 ...
Jessime Kirk's user avatar
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: ...
charlieb's user avatar
2 votes
1 answer
227 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. ...
Maryem Life's user avatar
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 ...
Soerendip's user avatar
  • 1,295
2 votes
1 answer
147 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 ...
fuad021's user avatar
  • 23
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, ...
Elisa's user avatar
  • 21
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 ...
Johnny Tam's user avatar
1 vote
0 answers
23 views

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 "...
Sashko Lykhenko's user avatar
1 vote
1 answer
87 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&...
Lance's user avatar
  • 143
1 vote
1 answer
142 views

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. ...
Lance's user avatar
  • 143
0 votes
1 answer
35 views

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 ...
micoay's user avatar
  • 11
0 votes
0 answers
117 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 ...
Kamil S Jaron's user avatar
0 votes
1 answer
949 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 ...
katara 's user avatar
  • 103
3 votes
1 answer
40 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 ...
rev.peter's user avatar
2 votes
0 answers
89 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 ...
Muhammad's user avatar
0 votes
1 answer
29 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 ...
variancekills's user avatar
-1 votes
1 answer
82 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 ...
Ehsan Salehabadi's user avatar
1 vote
0 answers
24 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 ...
HelpNeederStudent's user avatar
1 vote
2 answers
76 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 ...
Kamil S Jaron's user avatar
1 vote
1 answer
114 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: <...
pippo1980's user avatar
  • 1,088
1 vote
1 answer
70 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 ...
user257566's user avatar
1 vote
0 answers
46 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 ...
Art's user avatar
  • 111
1 vote
0 answers
45 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 ...
ibio_rep1's user avatar
1 vote
1 answer
43 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 ...
jasperhyp's user avatar
2 votes
3 answers
4k 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: ...
Fabricio's user avatar
9 votes
2 answers
776 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 ...
0x90's user avatar
  • 1,437
6 votes
1 answer
132 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 ...
Oren Milman's user avatar
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 ...
Reda's user avatar
  • 101
1 vote
0 answers
153 views

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 ...
user345394's user avatar
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 ...
dasfoogle's user avatar
0 votes
0 answers
39 views

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 ...
AlphaQueUp's user avatar