Bioinformatics tools extracted from a typical mammalian genome project [supplement]


eHIVE pipeline



ENSEMBL annotation pipeline


Bioinformatics tools extracted from a typical mammalian genome project

… resources like the SRA. They can be various different versioned downloaded data sets from ENSEMBL (version 67, 69, 70, or 73 here, but which were counted only once as ENSEMBL). It might be references to Reactome in a table.

With this broad definition in mind, Table 1 provides the list of named bioinformatics objects extracted from this project. The name or nickname or designation, the site at which it can be found (if available), and a publication or some citation is included …

BioMart news, and a shiny new look

… and is accessible from This tool enables enrichment analysis of genes in all Ensembl species and a broad range of gene identifiers for each species are also available. Furthermore, the tool supports cross-species analysis using Ensembl homology data. Finally, the enrichment tool facilitates analysis of BED files containing genomic features such as Copy Number Variations (CNVs) or Differentially Methylated Regions (DMRs).

The latest BioMart release comes with the new …

Saving your genome views: Ensembl (and UCSC Genome Browser, others)

In the latest update of Ensembl, the developers added the ability to save configurations. This allows you to set your  track views and analysis to a specific configuration and load that configuration at a later time. The blog post linked previously ( or here ) explains the steps to creating your own configurations you can save and return to. In the future they will be adding the ability to share your configurations …

NAR database issue (always a treasure trove)

… to many of the databases we know and love (links to go full text article): UCSC Genome Browser, Ensembl, UniProt, MINT, SMART, WormBase, Gene Ontology,   ENCODE, KEGG, UCSC Archaeal Browser,   IMG/M, DBTSS, InterPro  and others (we have tutorials on all those listed here).

And, as an indication of the explosion of data available (itself a subject of a database issue article, SRA ), there are a lot of new(ish) databases on specific datatypes such as MINAS, a …

Customization of views at Ensembl

… of upstate New York, in fact! So I won’t be able to write blog posts. Luckily Ewan Birney of Ensembl published one over the weekend that you should check out. In it he describes some of the newer features in Ensembl that will help you to group and show features in the human genome browser that you might be interested in. Check out his post:

Customising Ensembl Displays

Alternate sequences in UCSC and Ensembl

… that sequence. You can read more about the GRC haplotype and patch release at the site.

The Ensembl browser too of course has these alternative sequences included. Instead of going through how to access them here, I’ll point you to their very informative blog post on that very subject.




Tip of the Week: Varietas. A plaid database.

… to you.  If you check out the About page, you’ll see the source data available includes Ensembl, the NHGRI GWAS catalog, SNPedia, and GAD.  These sources also provide OMIM data, HGNC nomenclature, phenotypes, and MeSH terms. And the threads out include dbSNP, PubMed, SNPedia, and WikiGenes as well. This is also summarized nicely in Figure 1 of their paper.

It’s a very straightforward interface. There is a basic search with a text box for quick searching, and you select the type …

Tip of the Week: International Cancer Genome Consortium

… data and pull it down.  You may be familiar with BioMart from any number of places now ( Ensembl, Gramene, FlyBase, WormBase….more ).  But this is the first implementation of the new look–you are going to want to check that out.

For this week’s Tip of the Week you’ll see the ICGC site, and a quick query of the initial data that is available in the Data Coordination Center (DCC).  But this is just an appetizer.  Brace yourselves–the deluge is coming.

A Nature News …

Choosing a genome browser for your organism…

… existed.  One piece they specifically noted–when asked, many users did not say they used Ensembl, but the Ensembl software was the foundation of one of the items they did say they used.  MaizeGDB writes:

This result shows that users may not be aware of the underlying browser software that the various web sites use.

Ah, yeah.  Here’s another thing this shows: database end users are definitely not thinking about browser software the same way database developers are.  And I …