Categories: "Encode" or "Job Notes"

Next-Gen Sequence-Submissions to the ENA

June 3rd, 2009
New Sequencing results are submitted to the European Read Archive (ERA) - now called European Nucleotide Archive (ENA) which collaborates with the NCBI Short Read Archive (SRA). Documentation (EBI) General guidelines (NCBI) Meta data hierarchy:… more »

SourceAdaptor for Proserver DAS sources

January 28th, 2009
The Distributed Annotation System allows to share data across servers and applications. Example SourceAdaptor for Proserver DAS sources (complying to GENCODE format.) Example 1: Reading data from GFF file package Bio::Das::ProServer::SourceA… more »

Sanger Web-Proxy

November 20th, 2008
If you work at the Welcome Trust Sanger Institute and would like to browse web pages at home the same way you do at work, here is how to set it up: You need an ssh login, open a terminal window and connect like this ssh -L3128:webcache.sanger.ac.… more »

Gerp score

October 9th, 2008
GERP (Genomic Evolutionary Rate Profiling) "GERP identifies constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not… more »

CCDS

April 21st, 2008
The Consensus CoDing Sequence (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard… more »