Tag Archives: DBTSS

NAR database issue (always a treasure trove)

The advance access release of most of the  NAR database issue articles is out. As usual, this this database issue includes a wealth of new and updated data repositories and analysis tools. We’ll be writing up additional more extensive blog posts on it and doing some tips of the week over the next couple months, but I thought I’d highlight the issue and some of the reports:

There are a lot of updates 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 database of metal ions in nucleic acids (nice name :D); doRiNA, a database of RNA interactions in post-transcriptional regulation; BitterDB, a database of bitter compounds and well over 100 more.

And I’ll give a special shout out to my former PI at EMBL because I can, Peer Bork’s group has 4 databases listed in the issue: eggNOG, SMART, STITCH and OGEE. (and he and a couple members are on the InterPro paper also).

This is going to be a wealth of information to wade through!

UCSC Genome Browser: http://genome.ucsc.edu
Ensembl: http://www.ensembl.org/
UniProt: http://www.uniprot.org/
MINT: http://mint.bio.uniroma2.it/mint/
SMART: http://smart.embl.de/
WormBase: http://www.wormbase.org/
Gene Ontology: http://www.geneontology.org/
ENCODE: http://genome.ucsc.edu/ENCODE/
KEGG: http://www.kegg.jp
UCSC Archaeal Brower: http://archaea.ucsc.edu/
IMG: http://img.jgi.doe.gov/cgi-bin/w/main.cgi
DBTSS: http://dbtss.hgc.jp/
InterPro: http://www.ebi.ac.uk/interpro

 

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Updated Online Tutorials for DBTSS, Pfam and PDB

Seattle, WA (PRWEB) October 29, 2008 –  OpenHelix today announced the availability of newly updated tutorial suites on the DataBase of Transcriptional Start Sites (DBTSS), Pfam and the Protein Databank (PDB). DBTSS is a public resource for the analysis of promoter regions. Pfam is a comprehensive database of protein families manually created from multiple sequence alignments and hidden Markov models and PDB is a repository for a tremendous collection of structural information about proteins and other macromolecular structures. These three updated tutorials, in conjunction with the additional OpenHelix tutorials on ASTD, Entrez Protein and MMDB, give the researcher an excellent set of resources to carry their research from transcript to 3D protein structure.

The tutorial suites, available for single purchase or through a low- priced yearly subscription to all OpenHelix tutorials, contain a  narrated, self-run, online tutorial, slides with full script, handouts and exercises. With the tutorials, researchers can quickly learn to effectively and efficiently use these resources. These tutorials will teach users:

DBTSS

* to examine human promoter regions, and those in selected other species as well
* to locate transcription start sites, promoters, transcription factor binding sites and SNPs
* to use multiple query strategies to identify data of interest to your projects

Pfam

* a variety of ways to search Pfam, including by keyword or by protein sequence
* how to use the information in Pfam to predict functions for uncharacterized proteins
* where you can access domain interaction data in Pfam
* about Pfam Clans, which are groups of domains from a single evolutionary origin

PDB

* how to search for structures and related information using a variety of strategies
* to understand the results pages
* how to access various tools to visualize and examine structural details

To find out more about these and other tutorial suites visit the OpenHelix Tutorial Catalog and OpenHelix or  visit the OpenHelix Blog for up-to- date information on genomics.

About OpenHelix
OpenHelix, LLC, provides the genomics knowledge you need when you need  it. OpenHelix currently provides online self-run tutorials and on-site  training for institutions and companies on the most powerful and  popular free, web based, publicly accessible bioinformatics resources.  In addition, OpenHelix is contracted by resource providers to provide comprehensive, long-term training and outreach programs.