17 votes
Accepted

Publicly available genome sequence database for viruses?

There area few different influenza virus database resources: The Influenza Research Database (IRD) (a.k.a FluDB - based upon URL) A NIAID Bioinformatics Resource Center or BRC which highly curates ...
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15 votes
Accepted

How to convert species names into common names?

As Pierre mentioned, NCBI is a good resource for this kind of transformation. You can still use taxize to perform the conversion: ...
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14 votes

Are there any RepBase alternatives for genome-wide repeat element annotations?

Dfam has recently launched a sister resource, Dfam_consensus, whose stated aim is to replace RepBase. From the annoucement: Dfam_consensus provides an open framework for the community to store both ...
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14 votes

How to convert species names into common names?

use the NCBI taxon dump under ftp://ftp.ncbi.nih.gov/pub/taxonomy in taxdmp.zip you'll find all the names for a given NCBI taxon ...
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  • 1,473
9 votes

Designing a lab NGS file database schema

The Global Alliance for Genomics and Health has been working on the issue of representing sequencing data and metadata for storage and sharing for quite some time, though with mixed results. They do ...
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  • 429
9 votes
Accepted

Converting gene names from one public database format to another

I tend to use Ensembl Biomart for such queries since there are APIs for various programming languages, e.g. biomaRt, and, maybe more interestingly, via a REST API (although it’s a pretty terrible one)....
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8 votes

Converting gene names from one public database format to another

If you're comfortable doing a little programming, check out mygene.info (web services for gene annotations of all sorts). ID translation is specifically one of the use cases addressed in the ...
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  • 81
8 votes
Accepted

how to set database other than nr for remote blast+ search

I believe you're looking for env_nr? It's listed as such, under Metagenomic proteins in the blastp webpage. It appears that the ...
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8 votes
Accepted

How to get a list of genes corresponding to the list of SNPs (rs ids)?

I wonder if there is a simpler solution recently? (and hopefully, I can solve it within the scope of python. ) A simpler solution, I don't know... but this is at least one Python solution using ...
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  • 366
7 votes

Are there any RepBase alternatives for genome-wide repeat element annotations?

For pre-existing reliabe TE libraries it is a bit of a mess, because not everybody deposits the species-specific TE libraries to a database like RepBase. And as far as I know DFAM contains only human ...
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7 votes

Are there any databases of templates for common bioinformatic file formats?

You mention Biopython, which contains tests: https://github.com/biopython/biopython/tree/master/Tests. Some of the tests consist in reading files present in the folders listed in the above link. ...
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  • 2,930
7 votes

How to get a list of genes corresponding to the list of SNPs (rs ids)?

I can show you a simple way in R, using biomaRt. Let's say you have two snp ids you want to exmine. ...
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  • 3,521
7 votes
Accepted

Are these standard species abbreviations and how to look up others?

No, there are no standardized three-letter abbreviations for species names. Three-letter abbreviations with roman letters is 26^3 combinations, which is only 17,576 possible combinations. As a result ...
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  • 3,061
6 votes

Where is an up to date miRNA database and what happened to miRBase?

If you are still interested, last year miRBase generated new updates. Currently, according to ftp site the last release is 22.1. So, it is not a dead project and for more specific information you ...
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6 votes
Accepted

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

ChEBI It should be possible to get this information from the ChEBI database, see the exported tables. You could download the ontologies (in OWL / OBO), parse them using some ad-hoc parser or using a ...
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6 votes
Accepted

Is there any way of using biopython to write Swissprot files?

Using SeqIO.index rather than SeqIO.parse lets you read all the records into a dict, from ...
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  • 861
6 votes
Accepted

Human body sites knowledge base

I am the developer of Uberon and I would be happy to help you with what you need, either from Uberon, or from the FMA. You mentioned you need something simpler than FMA. There are a variety of tools ...
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  • 230
6 votes
Accepted

Do any publicly available databases detail protein structure and functional domains?

Some of this information (at least some domains, active sites, etc) is available from UniProt. If you want to download their whole database, you can search without specifying any terms and then click ...
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  • 315
6 votes

Are these standard species abbreviations and how to look up others?

These are not. The closest to "standard" is the 5-character abbreviation by Swissprot. It names 25,886 species and has been used for decades. It is also easy to remember for some common species such ...
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  • 5,645
6 votes

Is it possible to do this in R?

R supports logistic regression, which would seem to be the most efficient method for tackling this question. Assuming the "Chemo" variable is the type of chemo the code would be something like: <...
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  • 161
5 votes

Are there any databases of templates for common bioinformatic file formats?

Not that I am aware. It is best to go with format specifications when coding. Also it may be good to look at the example files that come together with various tools performing file conversions and ...
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  • 481
5 votes
Accepted

Designing a lab NGS file database schema

For metadata, I would use a SQL schema something like the following: ...
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  • 5,645
5 votes

Designing a lab NGS file database schema

I agree that there is no ideal data model that is going to be stable for very long in a quick-moving field like genome informatics. Perhaps a schema-less (NoSQL or some other document-based system, ...
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5 votes

Are there any RepBase alternatives for genome-wide repeat element annotations?

You could use RepeatScout, which has defined repeat libraries for a limited number of species (including human, mouse, and rat). If your taxon is not represented, you can also do de novo repeat ...
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  • 3,462
5 votes

how to find the bound form of an enzyme structure?

Tried looking for an explicit database? i.e. ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder: https://www.ncbi.nlm.nih....
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  • 602
5 votes
Accepted

Searching for gene expression data by cell line

Try the Gene Expression Omnibus - it looks like they have some datasets.
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5 votes
Accepted

Dataset: Locations of regulatory sequences in the human genome?

This can be done quite easily using Ensebl's BioMart. Choose the Ensembl Regulation database: Select the "Human Regulatory Features" dataset: That's basically it right there, just click on "...
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  • 7,957
5 votes

How can I find mutations associated with disease in human histone residues?

Ensembl contains this information: When you go to the “phenotype” menu item of a given gene, you will see a list of variants (potentially after clicking on “ALL associated variants”) with their ...
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5 votes

Is there a database of disease prevalence?

For rare diseases, you can use Orphanet. You can download an xml file with prevalence from orphadata. There is an OWL version of Orphanet called ORDO, you can browse it on the EBI Ontology Lookup ...
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  • 230
5 votes

Is there a database of disease prevalence?

Comment as an answer, as requested. The Incidence and Prevalance Database (IPD - subscription required).
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  • 646

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