JuncDB, Assembly, BioGPS and STITCH5

Dear all,

Today we discussed four papers in the literature meet

1. JuncDB: an exon–exon junction database

A database about the intron-exon boundaries within genes for comparing exonic architectures within sets of orthologous transcripts across 88 eukaryotic species

https://nar.oxfordjournals.org/content/44/D1/D101.full

2. Assembly: a resource for assembled genomes at NCBI

All the genome assemblies of a particular organism available at NCBI Refseq and INSDC databases are classified into four levels according to the degree to which they have been assembled 

1. Contig level assemblies that include only contigs
2. Scaffold level assemblies that include scaffolds and contigs
3. Chromosome level assemblies that include chromosomes or linkage groups, plus scaffolds and contigs
4. Complete genome assemblies in which all molecules are fully sequenced
   
   
   https://nar.oxfordjournals.org/content/44/D1/D73.full

 3. BioGPS: building your own mash-up of gene annotations and expression profiles

A gene annotation portal, which provides gene organisation, gene expression data from 6000 different datasets for nine model organisms (H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, D. rerio, A. thaliana, X. tropicalis and S. scrofa). 

https://nar.oxfordjournals.org/content/44/D1/D313.full

4. STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data

Information on protein-ligand interactions and their affinities derived from experiments or in silico analysis for 430 000 chemical and smore than 9 600 000 proteins.

https://nar.oxfordjournals.org/content/44/D1/D380.full