sequences, interaction networks and scientific literature
alfonso valencia (cnb)
Sequence analyses [Ras/p21 human sequence]
Server Description Example(s) BLAST similarity search Ras/p21 search, against Swiss-Prot. GeneQuiz automatic analyses of sequences
genome comparisonautomatic annotation of Ras/p21 COGs clustering of protein sequences in orthologous groups L17 (genomic context) genome comparison phylogenetic profiles
functional categoriesPFam, InterPro, Prosite domain identification and protein classification Ras/p21 in Pfam
Ras/p21 in InterProRecursive-blast and Ncut-clustering server sequence space exploration and protein family identification Result from a 3-round search (e-value threshold of 1e-07) with protein Ras/p21 in Swiss-Prot.
Protein interaction networks
Server Description Example(s) Interaction databases DIP interactions from experimental evidence (44.124) Ras/p21 (click on "graph") MIPS S. cerevisiae interactions (10.570: 9.030 physical and 1.540 genetic) (enter "YOR101W" in "search" box) BIND interactions (47.558 interactions, 1.441 complexes, 8 pathways) -tutorials- Ras/p21 PIMRider interactions in drosophila, HIV and H. pylori (registration required) - BRITE physical and genetic interactions (statistics) (enter "sce:YOR101W" in "search" box) intAct standards for interaction data -not yet Pathways BIOCYC several databases on metabolic pathways and genomes guided tour with tyrB KEGG genomes, metabolic pathways, regulatory pathways ras mediated signal transduction in yeast EMP enzymes and metabolic pathways - Repositories of predicted protein interactions ecid predictions for E. coli with several methods predictions for FtsH STRING predictions with several methods for 110 genomas (based on COGs) predictions for COG1117 AllFuse prediction of funcional associations btween proteins, in complete genomes protein TM1826 PLEX construction and comparison of phylogenetic profiles -
Scientific literature
Server Description Example(s) PubMed search in scientific literature (12 millon of articles) find papers connecting Ras/p21 with cancer: use, for example: "ras AND p21 AND (tumor or cancer)" in search window) Alma TextMiner extraction and representation of knowledge from scientific literature (user: Ab113895 - password: ed231935) - ihop exploration of the information network derived from literature: phenotypes, pathologies, function... through proteins -
Federico Abascal, 4 de febrero de 2004