02607nas a2200181   4500008004100000245009100041210006900132300001200201490000700213520184100220653007402061653005202135653007802187100001602265700002302281700001502304856010602319       2005                        eng d00aHighly specific and accurate selection of siRNAs for high-throughput functional assays0 aHighly specific and accurate selection of siRNAs for highthrough  a1376-820 v213 aMOTIVATION: Small interfering RNA (siRNA) is widely used in functional genomics to silence genes by decreasing their expression to study the resulting phenotypes. The possibility of performing large-scale functional assays by gene silencing accentuates the necessity of a software capable of the high-throughput design of highly specific siRNA. The main objective sought was the design of a large number of siRNAs with appropriate thermodynamic properties and, especially, high specificity. Since all the available procedures require, to some extent, manual processing of the results to guarantee specific results, specificity constitutes to date, the major obstacle to the complete automation of all the steps necessary for the selection of optimal candidate siRNAs. RESULT: Here, we present a program that for the first time completely automates the search for siRNAs. In SiDE, the most complete set of rules for the selection of siRNA candidates (including G+C content, nucleotides at determined positions, thermodynamic properties, propensity to form internal hairpins, etc.) is implemented and moreover, specificity is achieved by a conceptually new method. After selecting possible siRNA candidates with the optimal functional properties, putative unspecific matches, which can cause cross-hybridization, are checked in databases containing a unique entry for each gene. These truly non-redundant databases are constructed from the genome annotations (Ensembl). Also intron/exon boundaries, presence of polymorphisms (single nucleotide polymorphisms) specificity for either gene or transcript, and other features can be selected to be considered in the design of siRNAs. AVAILABILITY: The program is available as a web server at http://side.bioinfo.cnio.es. The program was written under the GPL license. CONTACT: jdopazo@cnio.es.10a*Algorithms Base Sequence *Gene Silencing Molecular Sequence Data RNA10aRNA/*methods *Software *User-Computer Interface10aSmall Interfering/*genetics Sequence Alignment/*methods Sequence Analysis1 aSantoyo, J.1 aVaquerizas, J., M.1 aDopazo, J.  uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1559135701756nas a2200145   4500008004100000245011900041210006900160300001200229490001500241520120200256100001501458700001601473700001501489856010601504       2004                        eng d00aPhylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species0 aPhylogenomics and the number of characters required for obtainin  ai116-210 v20 Suppl 13 a<p>MOTIVATION: Through the most extensive phylogenomic analysis carried out to date, complete genomes of 11 eukaryotic species have been examined in order to find the homologous of more than 25,000 amino acid sequences. These sequences correspond to the exons of more than 3000 genes and were used as presence/absence characters to test one of the most controversial hypotheses concerning animal evolution, namely the Ecdysozoa hypothesis. Distance, maximum parsimony and Bayesian methods of phylogenetic reconstruction were used to test the hypothesis. RESULTS: The reliability of the ecdysozoa, grouping arthropods and nematodes in a single clade was unequivocally rejected in all the consensus trees. The Coelomata clade, grouping arthropods and chordates, was supported by the highest statistical confidence in all the reconstructions. The study of the dependence of the genomes’ tree accuracy on the number of exons used, demonstrated that an unexpectedly larger number of characters are necessary to obtain robust phylogenies. Previous studies supporting ecdysozoa, could not guarantee an accurate phylogeny because the number of characters used was clearly below the minimum required.</p>1 aDopazo, H.1 aSantoyo, J.1 aDopazo, J.  uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1526278902164nas a2200229   4500008004100000245009400041210006900135300001100204490000700215520128900222653008201511653001201593653009301605100001401698700002301712700001601735700002401751700002201775700001601797700001501813856010601828       2004                        eng d00aPupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level0 aPupaSNP Finder a web tool for finding SNPs with putative effect   aW242-80 v323 aWe have developed a web tool, PupaSNP Finder (PupaSNP for short), for high-throughput searching for single nucleotide polymorphisms (SNPs) with potential phenotypic effect. PupaSNP takes as its input lists of genes (or generates them from chromosomal coordinates) and retrieves SNPs that could affect the conserved regions that the cellular machinery uses for the correct processing of genes (intron/exon boundaries or exonic splicing enhancers), predicted transcription factor binding sites (TFBS) and changes in amino acids in the proteins. The program uses the mapping of SNPs in the genome provided by Ensembl. Additionally, user-defined SNPs (not yet mapped in the genome) can be easily provided to the program. Also, additional functional information from Gene Ontology, OMIM and homologies in other model organisms is provided. In contrast to other programs already available, which focus only on SNPs with possible effect in the protein, PupaSNP includes SNPs with possible transcriptional effect. PupaSNP will be of significant help in studies of multifactorial disorders, where the use of functional SNPs will increase the sensitivity of identification of the genes responsible for the disease. The PupaSNP web interface is accessible through http://pupasnp.bioinfo.cnio.es.10aAmino Acid Substitution Binding Sites Humans Internet Phenotype *Polymorphism10aGenetic10aSingle Nucleotide RNA Splicing *Software Transcription Factors/metabolism *Transcription1 aConde, L.1 aVaquerizas, J., M.1 aSantoyo, J.1 aAl-Shahrour, Fatima1 aRuiz-Llorente, S.1 aRobledo, M.1 aDopazo, J.  uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1521538801500nas a2200217   4500008004100000245007700041210006900118300001100187490000700198520080200205653001001007653002901017100001601046700002401062700002101086700001501107700002301122700001601145700001501161856010601176       2003                        eng d00aGEPAS: A web-based resource for microarray gene expression data analysis0 aGEPAS A webbased resource for microarray gene expression data an  a3461-70 v313 a<p>We present a web-based pipeline for microarray gene expression profile analysis, GEPAS, which stands for Gene Expression Profile Analysis Suite (http://gepas.bioinfo.cnio.es). GEPAS is composed of different interconnected modules which include tools for data pre-processing, two-conditions comparison, unsupervised and supervised clustering (which include some of the most popular methods as well as home made algorithms) and several tests for differential gene expression among different classes, continuous variables or survival analysis. A multiple purpose tool for data mining, based on Gene Ontology, is also linked to the tools, which constitutes a very convenient way of analysing clustering results. On-line tutorials are available from our main web server (http://bioinfo.cnio.es).</p>10agepas10amicroarray data analysis1 aHerrero, J.1 aAl-Shahrour, Fatima1 aDiaz-Uriarte, R.1 aMateos, A.1 aVaquerizas, J., M.1 aSantoyo, J.1 aDopazo, J.  uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1282434500715nas a2200181   4500008004100000245013000041210006900171260003000240300001000270653001500280100002400295700001600319700001500335700001600350700002100366700001500387856013100402       2003                        eng d00aUsing Gene Ontology on genome-scale studies to find significant associations of biologically relevant terms to group of genes0 aUsing Gene Ontology on genomescale studies to find significant a  aNew York, USAbIEEE Press  a43-5210ababelomics1 aAl-Shahrour, Fatima1 aHerrero, J.1 aMateos, A.1 aSantoyo, J.1 aDíaz-Uriarte, R1 aDopazo, J.  uhttp://clinbioinfosspa.es/content/using-gene-ontology-genome-scale-studies-find-significant-associations-biologically-relevant