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 ...
- 286
15
votes
Accepted
8
votes
Accepted
Missing data mappings in mygene.info while trying to convert Genes Ensembl Ids to Entrez Ids
As others have mentioned in their answer, bioMart is usually the best place to go for this infomation because it draws its data directly from the Ensembl database.
However, you will find you do not ...
- 3,271
8
votes
8
votes
Accepted
How to extract RNA sequence and secondary structure restrains from a PDB file
I suggest you take a look at rna-pdb-tools we do way more than you need! :-) The tools can get you a sequence, secondary structure and much more using various ...
- 676
7
votes
Accepted
Given a VCF of a human genome, how do I assess the quality against known SNVs?
To achieve (at least some of) your goals, I would recommend the Variant Effect Predictor (VEP). It is a flexible tool that provides several types of annotations on an input .vcf file. I agree that ...
- 366
7
votes
Accepted
Database of copy number alterations in different cancer types
I don't know if there's a database that does exactly what you want, but there are some places that might help you figure this out, especially if you already have a list of CNAs/genes/regions in mind.
...
- 535
7
votes
Accepted
Converting Ensembl Gene IDs to Entrez Gene IDs through biomart
The ID you need is the NCBI gene ID, which is the same as the EntrezGene ID.
- 3,271
7
votes
Accepted
Retrieve detailed gene descriptions
MyGene.info
Using the R package for the MyGene.info database:
...
- 2,624
7
votes
Retrieve detailed gene descriptions
Description of how to use biomaRt here. Filter by your list of gene IDs. Get the descriptions etc as attributes. Eg:
...
- 1,749
7
votes
How do you query and explore ENCODE data?
I don't know whether there is an API, but ENCODE's website does provide an interactive data matrix where you can filter data based on assay and sample type, place data sets in a "shopping cart", and ...
- 5,060
6
votes
Accepted
Human Cell Atlas - Data availability
There is now a post on Biostars:
We are starting to define the release process for the Human Cell
Atlas.
The first couple of HCA releases will be primarily single-cell RNA-Seq
and we are ...
- 2,159
6
votes
Accepted
How can I reproduce a manual NCBI search with Biopython Entrez module?
This can be done by using the "Search details" as a search term in Entrez.esearch:
...
- 3,090
5
votes
Accepted
hg38 GTF file with RefSeq annotations
You will probably be interested in the following UCSC wiki page, which explains how to go from most of the UCSC tables to GTF/GFF:
http://genomewiki.ucsc.edu/index.php/Genes_in_gtf_or_gff_format
The ...
- 171
5
votes
Given a VCF of a human genome, how do I assess the quality against known SNVs?
The greatest protein coding variant catalogue is definitely ExAC (>65k individuals). They also published a blogpost where they describe how to reproduce figures in the paper (it is a good start how to ...
- 5,497
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 ...
- 230
5
votes
Is there a database of disease prevalence?
Comment as an answer, as requested.
The Incidence and Prevalance Database (IPD - subscription required).
- 646
5
votes
Accepted
What is the ICGC normalized_read_count?
By reading this thread on seqanswers and by comparing the data to TCGA, I figured out
raw_read_count is the read count which you use as input for e.g. ...
- 273
5
votes
How to export web NCBI tBLASTn results in table format with many queries?
It sounds like your easiest option is to just install blast on your local machine and set up the databases there. It really will only take a few minutes to blast 6,000 sentences against a yeast genome ...
- 3,141
5
votes
How do you query and explore ENCODE data?
You can just add /?format=json to any page to get the JSON output.
ENCODE REST API documentation: https://www.encodeproject.org/help/rest-api/
Example scripts: ...
- 2,159
5
votes
Accepted
How to get the number of complete phage genomes available on ncbi?
Go to the NCBI nuccore database, at https://www.ncbi.nlm.nih.gov/nuccore
Copy and paste the search term:
...
M__♦
- 11.2k
4
votes
How to extract RNA sequence and secondary structure restrains from a PDB file
Context
The PDB file format is a fixed-column file format designed in 1970s for storing structural models of macromolecules. The format has been around for long time, has many uses, and although it ...
- 1,241
4
votes
Given a VCF of a human genome, how do I assess the quality against known SNVs?
Your best bet is to use programs that provide you an complete annotation of variants present in your VCF. Two examples are snpEff and Annovar. These programs work on known variants deem different ...
- 182
4
votes
Accepted
How to select a cutoff for interaction confidence in STRINGdb?
I have used STRING pretty heavily, and have compared it to various other databases of protein interactions and signaling pathways. I do feel like it has a lot of quality interaction annotations, but ...
- 429
4
votes
How to select a cutoff for interaction confidence in STRINGdb?
This depends on what you are trying to do and whether you value specificity over sensitivity. We can't tell you since it is entirely dependent on the biological question you want to answer.
However, I ...
- 9,442
4
votes
Publicly available genome sequence database for viruses?
In addition to what others have suggested, I would also recommend PaVE as a resource. This is a curated database maintained by the NIAID and current holds over 300 papilloma virus genomes.
- 255
4
votes
Accepted
Bioperl - how can i print first result of search sequence per iteration?
In the simplest case, if you just want to stop after the first record was printed, you can just add exit (I also corrected the syntax errors you had and added ...
- 9,442
4
votes
How to obtain .bed file with coordinates of all genes
You can indeed get this information from the UCSC Table Browser. Select knownGene as your primary table, make a filter, add knownCanonical to as a linked table to filter on, then in the free-form ...
- 171
4
votes
Accepted
How to determine the primary Uniprot accession number from a set of accession numbers?
Reposting my answer from the related ticket in the Biology section:
I think there is an issue with the terminology. The "primary" accession number, is the first accession number in cases where an ...
4
votes
Automating sequence download from Wormbase
Further inspecting the source code of the downloaded page, I found the following:
...
- 3,090
Only top scored, non community-wiki answers of a minimum length are eligible