Our Company resources

11-09-2012

Programming Tools
Public Resources

Biocoders Hub

A community for sharing bioinformatics source code with other specialists. 

http://www.biocodershub.net

09-10-2012

Programming Tools
Public Resources

Bioconductor

Bioconductor is an open source and open development software project that aims to provide access to a wide range of powerful statistical and graphical methods for the analysis of genomic data.

http://www.bioconductor.org/

09-10-2012

Programming Tools
Public Resources

BioMoby

BioMOBY is an international research project involving biological data hosts, biological data service providers, and coders whose aim is to explore various methodologies for biological data representation, distribution, and discovery.

http://www.biomoby.org

09-10-2012

Databases
Public Resources

BioNumbers

BioNumbers (http://www.bionumbers.hms.harvard.edu) is a database of key numbers in molecular and cell biology--the quantitative properties of biological systems of interest to computational, systems and molecular cell biologists. Contents of the database range from cell sizes to metabolite concentrations, from reaction rates to generation times, from genome sizes to the number of mitochondria in a cell. All numbers are taken directly from a literature source and that reference is provided with the number.

http://www.bionumbers.hms.harvard.edu

09-10-2012

Databases
Public Resources

CharProtDB

CharProtDB is a curated database of biochemically characterized proteins. The initial data set in CharProtDB was collected through manual literature curation, and has been expanded by importing selected records from publicly available protein collections. Annotations in CharProtDB include gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession.

http://www.jcvi.org/charprotdb/index.cgi/home

09-10-2012

Databases
Public Resources

iRefWeb

A web interface to data on protein-protein interactions (PPI) consolidated from major public databases. Consolidates by mapping protein IDs across databases. Researchers can gauge reliability of an interaction using simple criteria (eg. number of supporting publications, high- or low-throughput) or detection methods used in the original experiments. Compare and contrast the PPI information extracted from the same publications by different databases.

http://wodaklab.org/iRefWeb/

09-10-2012

Databases
Public Resources

UKPMC

UK PubMed Central (UKPMC) is a full-text article database that extends the functionality of the original PubMed Central (PMC) repository. Now includes both a UKPMC and PubMed search, as well as access to other records such as Agricola, Patents and recent biomedical theses. UKPMC also differs from PubMed/PMC in that the full text and abstract information can be searched in an integrated manner from one input box. Furthermore, UKPMC contains 'Cited By' information as an alternative way to navigate the literature and has incorporated text-mining approaches to semantically enrich content and integrate it with related database resources. Finally, UKPMC also offers added-value services (UKPMC+) that enable grantees to deposit manuscripts, link papers to grants, publish online portfolios and view citation information on their papers.

http://www.ukpmc.ac.uk

09-10-2012

Web Services
Public Resources

BioBIKE

BioBIKE is a web-based environment enabling biologists with little programming expertise to combine tools, data and knowledge in novel and complex ways. BioBIKE is composed of three components: a biological knowledge base, a graphical programming interface and an extensible set of tools. Users may also invent their own tools.

http://www.Biobike.org

09-10-2012

Programming Tools
Public Resources

BioSmalltalk

BioSmalltalk is an open source library for doing bioinformatics with Smalltalk. The goal of BioSmalltalk is to concile the benefits of a pure object environment with bioinformatics related tasks, so life scientists (or non-professional programmers) could reach their objectives programming fast and easily and without the complexities of typical programming environments.

http://code.google.com/p/biosmalltalk/

07-01-2013

Comparative Genomics
Public Resources

agriGO

agriGO is an integrated gene ontology analysis toolkit for the agriculture community. Supported organisms and gene identifiers were expanded over EasyGO tool, and several tools for predicting gene function are included.

http://bioinfo.cau.edu.cn/agriGO/

07-01-2013

Comparative Genomics
Public Resources

ATIVS

ATIVS (analytical tool for influenza virus surveillance) is a web server for analyzing serological data of all influenza viruses and provide interpretive summaries. ATIVS also compares the HA1 sequences of viruses to those of the reference vaccine strains to predict influenza A/H3N2 antigenic drift.

http://influenza.nhri.org.tw/ATIVS/

07-01-2013

Comparative Genomics
Public Resources

CGView Server

The CGView Server generates graphical maps of circular genomes that can be used to visualize sequence conservation in the context of sequence features, imported analysis results, open reading frames and base composition plots. The server uses BLAST to compare the primary sequence of up to three genomes or sequence sets, aiding in the identification of conserved genome segments, instances of horizontal transfer or visualization of genome segments from newly obtained sequence reads.

http://stothard.afns.ualberta.ca/cgview_server/

07-01-2013

Comparative Genomics
Public Resources

CisMols

CisMols (Cis-regulatory Modules) is a tool that identifies compositionally predicted cis-clusters that occur in groups of co-regulated genes within each of their ortholog-pair evolutionarily conserved cis-regulatory regions.

http://cismols.cchmc.org/

07-01-2013

Comparative Genomics
Public Resources

CoMet

CoMet is a web server for comparative metagenomics, and is particularly suited for analysis of large collections of metagenomic short read data.

http://comet.gobics.de

26-09-2013

GO Annotation Tools
Public Resources

Blast2GO

Blast2GO (B2G) joins in one universal application similarity search based GO annotation and functional analysis. B2G offers the possibility of direct statistical analysis on gene function information and visualization of relevant functional features on a highlighted GO direct acyclic graph (DAG). Furthermore B2G includes various statistics charts summarizing the results obtained at BLASTing, GO-mapping, annotation and enrichment analysis (Fisher's Exact Test). All analysis process steps are configurable and data import and export are supported at any stage. The application also accepts pre-existing BLAST or annotation files and takes them to subsequent steps. The tool offers a very suitable platform for high throughput functional genomics research in non-model species. B2G is a species-independent, intuitive and interactive desktop application which allows monitoring and comprehending the whole annotation and analysis process supported by additional features like GO Slim integration, evidence code (EC) consideration, a Batch-Mode or GO-Multilevel-Pies.

http://www.blast2go.org/

26-09-2013

GO Annotation Tools
Public Resources

g:Profiler

g:Profiler is a public web server for characterising and manipulating gene lists resulting from mining high-throughput genomic data. g:Profiler has a simple, user-friendly web interface with powerful visualisation for capturing Gene Ontology, pathway, or transcription factor binding site enrichments down to individual gene levels. Besides standard multiple testing corrections, a new improved method for estimating the true effect of multiple testing over complex structures like GO has been introduced. Interpreting ranked gene lists is supported from the same interface with very efficient algorithms. Such ordered lists may arise when studying the most significantly affected genes from high-throughput data or genes co-expressed with the query gene. Other important aspects of practical data analysis are supported by modules tightly integrated with g:Profiler. These are: g:Convert for converting between different database identifiers; g:Orth for finding orthologous genes from other species; and g:Sorter for searching a large body of public gene expression data for co-expression. g:Profiler supports 31 different species, and underlying data is updated regularly from sources like the Ensembl database. Bioinformatics communities wishing to integrate with g:Profiler can use alternative simple textual outputs.

http://biit.cs.ut.ee/gprofiler/

26-09-2013

GO Annotation Tools
Public Resources

GeneTools

GeneTools is a collection of web-based tools that brings together information from a broad range of resources, and provides this in a manner particularly useful for genome-wide analyses. Today, the two main tools connected to this database are the NMC Annotation Database V2.0 and eGOn V2.0 (explore Gene Ontology). The NMC Annotation Database V2.0 provides information from UniGene, EntrezGene, SwissProt and Gene Ontology (GO).

http://www.genetools.microarray.ntnu.no/common/intro.php

26-09-2013

GO Annotation Tools
Public Resources

GOanna

GOanna is used to find annotations for proteins using a similarity search. The input can be a list of IDs or it can be a list of sequences in FASTA format. GOanna will retrieve the sequences if necessary and conduct the specified BLAST search against a user-specified database. The resulting file contains GO annotations of the top BLAST hits. The sequence alignments are also provided so the user can use these to access the quality of the match.

http://agbase.msstate.edu/GOAnna.html

26-09-2013

GO Annotation Tools
Public Resources

GoAnnotator

GoAnnotator is a tool for verification of electronic protein annotations using GO terms automatically extracted from literature.

http://xldb.fc.ul.pt/biotools/rebil/goa/

26-09-2013

GO Annotation Tools
Public Resources

Gene Ontology Categorizer (GOCat)

The Gene Ontology Categorizer (GOCat) is an automatic text categorizer. The tool classifies any input text (a few words, an abstract, a set of PubMed Identifiers...) into Gene Ontology categories. The system, originally developed for the first BioCreative evaluation campaign, aims at facilitating functional annotation of gene and gene products using text mining methods. For every predicted category, a confidence score and a short text passage, extracted from the input text, are provided. The interface can also be used to navigate the Gene Ontology thanks to direct Quick GO links.

http://eagl.unige.ch/GOCat/

26-09-2013

GO Annotation Tools
Public Resources

Gene Ontology for Motifs (GOMO)

Gene Ontology for Motifs (GOMO) is an alignment- and threshold-free comparative genomics approach for assigning functional roles to DNA regulatory motifs from DNA sequence. The algorithm detects associations between a user-specified DNA regulatory motif (expressed as a position weight matrix; PWM) and Gene Ontology terms.

http://meme.nbcr.net/

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