17 votes
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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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13 votes
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How to obtain .bed file with coordinates of all genes

Via Gencode and BEDOPS convert2bed: ...
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8 votes
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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 ...
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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 ...
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  • 366
7 votes
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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 ...
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  • 3,211
7 votes
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Retrieve detailed gene descriptions

MyGene.info Using the R package for the MyGene.info database: ...
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  • 2,574
7 votes
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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. ...
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7 votes

Converting Ensembl Gene IDs to Entrez Gene IDs through biomart

Conversion using R: ...
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  • 2,574
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: ...
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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 ...
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6 votes
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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.
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  • 3,211
6 votes
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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 ...
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  • 2,099
6 votes
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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: ...
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  • 2,960
5 votes
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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 ...
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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 ...
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  • 5,287
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
5 votes
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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. ...
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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: ...
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  • 2,099
5 votes
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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: ...
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  • 7,284
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 ...
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  • 1,066
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 ...
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  • 182
4 votes
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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 ...
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  • 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 ...
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  • 8,111
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.
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  • 255
4 votes
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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 ...
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  • 8,111
4 votes
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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 ...
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4 votes

Automating sequence download from Wormbase

Further inspecting the source code of the downloaded page, I found the following: ...
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  • 2,960
4 votes

How to get all PDB homologs from Uniprot (mapping + BLAST)?

For the correspondence between PDB and Uniprot entries you can use SIFTS -- a semi-automated mapping between PDB and UniProt maintained by PDBe. The pipeline that creates the mappings uses BLAST and ...
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  • 1,066
4 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 ...
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  • 3,071

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