Bioinformatic Department Tools
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GEPAS: A web-based tool for microarray data analysis and interpretation
GEPAS is one of the most complete and extensively used web-based packages for microarray data analysis. During its more than 5 years of activity it has continuously been updated to keep pace with the state-of-the-art in the changing microarray data analysis arena.
GEPAS offers diverse analysis options that include well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and functional profiling of the experiment. New options for time-course (or dose-response) experiments, microarray-based class prediction, new clustering methods and new tests for differential expression have been included. The new pipeliner module allows automating the execution of sequential analysis steps by means of a simple but powerful graphic interface.
An extensive re-engineering of GEPAS has been carried out which includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. GEPAS is nowadays the most quoted web tool in its field and it is extensively used by researchers of many countries and its records indicate an average usage rate of 500 experiments per day. GEPAS, is available at http://www.gepas.org.
more info at: http://bioinfo.cipf.es/wikigepas/
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments
Babelomics is a complete suite of web tools for the functional profiling of genome scale experiments, with new and improved methods as well as more types of functional definitions. Babelomics includes different flavours of conventional functional enrichment methods as well as more advanced gene set analysis methods that makes it a unique tool among the similar resources available.
In addition to the well-known functional definitions (GO, KEGG), Babelomics includes new ones such as Biocarta pathways or text mining-derived functional terms. Regulatory modules implemented include transcriptional control (Transfac, CisRed) and other levels of regulation such as miRNA-mediated interference. Moreover, Babelomics allows for sub-selection of terms in order to test more focused hypothesis. Also gene annotation correspondence tables can be imported, which allows testing with user-defined functional modules.
Babelomics contains one of the most cited tools in the field of functional enrichment analysis, the FatiGO. See quotation in ScienceWatch.
Finally, a tool for the ‘de novo’ functional annotation of sequences has been included in the system. This allows using yet unannotated organisms in the program. Babelomics has been extensively re-engineered and now it includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. Babelomics is available at http://www.babelomics.org
more info at: http://babelomics.bioinfo.cipf.es
SNOW: studying Networks in the Omic World
SNOW stands for "Studying Networks in the Omic World" and complements tools such as FatiGO and Marmite (Babelomics suite) introducing a new dimension in the functional profiling of high-throughput experiments results, this is, protein-protein interaction data. SNOW extracts and evaluates the cooperative behavior of lists of selected proteins/genes using the interactome as scaffold.SNOW identifies hubs and evaluates the global degree of connections, centrality and neighborhood aggregation of the list by comparing the distributions of nodes connections degree, betweenness centrality and clustering coefficient respectively against the complete distribution of these parameters into the interactome of reference. Besides this, SNOW extracts the minimum network that connects the proteins/genes in the list. A user-fixed number of external proteins to connect nodes in the list is allowed. The topology of this network is evaluated by comparing distributions of graph parameters of this network against pre-calculated distributions of a set (10000) of random lists with same size range. By this, SNOW extracts information about whether the network represented in the list has more hubs, is more connected or has a more regular connections distribution than a random network.SNOW also provides an interactive visualization of the network and a complete description of interactomic and local network parameters of each protein/gene in the list as well as the external nodes introduced by the program. This information together with the functional annotation provided will guide the user to identify the important nodes within, or even outside, the list as well as evaluate the modular functionality of the list as an entity.
more info at: http://snow.bioinfo.cipf.es
Blast2GO: A universal Gene Ontology annotation, visualization and analysis tool for functional genomics research
Blast2GO is an "all-in-one" tool for functional annotation of (novel) sequences and the analysis of annotation data. Blast2GO is designed for experimentalists in a user friendly manner. An intuitive interface, the many graphical parameters and the detailed users manual makes the use of the tool possible from the first try. Blast2GO is easy to start up and low in maintenance. Make sure you have JAVA installed, download Blast2GO from its site and start using the application. Updates are automatic. Blast2GO is high-throughput and interactive. It can annotate several thousands of sequences in one session. Users can follow and modify the annotation process at any stage with this highly configurable, functional annotation workstation. You can design your costum annotation style through the many configurable parameters. Statistical charts are available to guide users in the annotation process. Functional annotation is performed throguh three steps. Blast2GO supports different vocabulaires like Gene Ontology, KEGG maps, InterPro and Enzyme Codes. For Gene Ontology funcional annotation follow 3 application steps: BLAST againts a public or private databases. Do mapping against GO resources to fetch functional data. Perform annotation to generate trustful functional assingments. Blast2GO does not only generate funcional annotations. Data Mining features allow to interrogate the biological meaning of your data with different graphical and statistical functions. Blast2GO is used by more than hundred labs worldwide, has contributed to the annotation efforts in EST projects, genomics studies and microarray experiments, covering taxa from microorganisms to fungi, plants, fish, animals and humans. In the last two year the application has been cited in more than 100 scientific papers.
more info at: http://www.blast2go.org
Pupasuite: SNP prioritization for large scale genotyping and functional characterization of SNPs in next generation sequencing experiments
PupaSuite is a web tool for the selection of SNPs with potential phenotypic effect, oriented to help in the design of large-scale genotyping projects and to the characterization of new SNPs from next generation technologies.
PupaSuite uses a collection of data on SNPs from heterogeneous sources and a large number of pre-calculated predictions to offer a flexible and intuitive interface for selecting an optimal set of SNPs. It implements new facilities such as the analysis of user's data to derive haplotypes with functional information. A new estimator of putative effect of polymorphisms has been included that uses evolutionary information. Also SNPeffect database predictions have been included.
PupaSuite 2 can input lists of SNPs, genes, or chromosomal regions and produce lists of SNPs with their possible phenotypic effect. Moreover, it can also calculate haplotypes and estimate the possible functionality of the corresponding combinations of SNPs.
PupaSuite can also produce graphic interactive analyses of single genes. There, a filter allows displaying SNPs potentially causing different types (structural, regulatory, splicing, etc.) and degrees of alterations.
The PupaSuite web interface is accessible through http://pupasuite.bioinfo.cipf.es and through http://www.pupauite.org.
more info at: http://pupasuite.bioinfo.cipf.es
Phylemon: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypothesis testing
Phylemon 2.0 is the second release of the suite of web-tools for molecular evolution, phylogenetics and phylogenomics. It is conceived as a natural response to the increasing demand of data analysis of experimental scientists seeking to add molecular evolution and phylogenetic insight into their research.
Phylemon 2.0 has several features that differentiate it from other web resources: (i) It offers an integrated environment that enables the direct concatenation of evolutionary analyses, format conversions, the storage and edition of projects and results, (ii) Phylemon suggests the next possible analyses, thus guiding the user and facilitating the integration of multi-step analyses, and (iii) users can define and save pipelines for specific phylogenetic analysis to be used on many genes in subsequent sessions or multiple genes in a single session (phylogenomics).
The new web server integrates a suite of more than 30 different tools such as sequence alignment of long genomic regions, alignment refinement, tree reconstruction by distances using the best DNA model explaining the data, DNA model selection and averaging using the jModelTest and HyPhy tools to test for molecular adaptation considering synonymous rate variation across sites. Phylemon 2.0 has been completely re-engineered improving job submission, project, file, and task management.
more info at: http://phylemon.bioinfo.cipf.es
DBAli: a database of pairwise and multiple protein structure alignments
Advances in structural biology have resulted in a rapid increase in the number of experimentally determined protein structures. There is a need for an up-to-date comprehensive database of pairwise and multiple structure-based alignments for families of related proteins as well as tools to automatically and comprehensively generate, store, and analyze these alignments. We aim to provide some of this functionality to the biological community.
DBAli stores pairwise comparisons of all structures in the Protein Data Bank calculated using the program MAMMOTH. It also contains multiple structure alignments generated by the SALIGN command of MODELLER. DBAli is updated weekly. As of August 2007, DBAli contains ~1.7 billion pairwise comparisons and over 12,500 family-based multiple structure alignments for ~35,000 non-redundant protein chains in the PDB.
DBAli, a database of pairwise and multiple structure alignments, also integrates tools for dynamically establishing relationships between protein structures and their fragments. The utility of the database is illustrated by outlining several of its current applications. The DBAli database is accessible via the World Wide Web at http://www.dbali.org
more info at: http://www.dbali.org
SARA: a server for function annotation of RNA structures
Recent interest in non-coding RNA transcripts has resulted in a rapid increase of deposited RNA structures in the Protein Data Bank. However, a characterization and functional classification of the RNA structure and function space have only been partially addressed. Here, we introduce the SARA program for pairwise alignment of RNA structures as a web server for structure-based RNA function assignment.
The SARA server relies on the SARA program, which aligns two RNA structures based on a unit-vector root mean square approach. The likely accuracy of the SARA alignments is assessed by three different p-values estimating the statistical significance of the sequence, secondary structure and tertiary structure identity scores, respectively. Our benchmarks, which relied on a set of 419 RNA structures with known SCOR structural class, indicate that at a negative logarithm of mean p-value of 2.5 or higher, SARA can assign the correct or a similar SCOR class to 81.4% and 95.3% of the benchmark set, respectively.
The SARA server is freely accessible via the World Wide Web at http://sgu.bioinfo.cipf.es/
more info at: http://sgu.bioinfo.cipf.es/services/SARA
