Open Directory - Science: Biology: Bioinformatics: Online Services
See also: - Very helpful software for locating and displaying transcription factor binding sites within DNA sequences - from the Univ. of Penn. - An interesting tool to discover and visualize over- or under-represented words in genetic sequences. Requires Java support in browser. Also available as a downloadable program. - Online program that calculates the distribution of offspring genotypes from dominant, codominant and recessive gene crosses, for up to 6 genes. - The focus of the GBF project "Molecular Bioinformatics of Gene Regulation" are regulatory genomic signals and regions that govern transcriptional control based on TRANSFAC - The Transcription Factor Database. It compiles data about gene regulatory DNA sequences and protein factors binding to and acting through them. - Service for the identification of bacteria and fungi sequences by sequence alignment. - Provides a collection of information on data sources for biological networks, file formats that save biological networks and software to analyze the information of these sources. - Database of genetic and physical interactions. It contains interaction data from many sources, including several genome/proteome-wide studies, the MIPS database, and BIND. - Resource for storing, searching and retrieving published mathematical models of biological interests. Models present in BioModels Database are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc. - Tools and methods for computational biology. Working on secondary protein structure prediction, providing reliable profiles, and developing new ways to study molecular biology through bioinformatics. - BIND is a database designed to store full descriptions of interactions, molecular complexes and pathways. - Scientists at the Broad Institute have developed a range of software tools for the analysis of increasingly large genome-related datasets. These are openly available to the scientific community. - We provide bioinformatics support, services, servers, and software to Canadian researchers. - A free software tool for analysing the hypothetical secondary structure of a family of homologous RNA. - User guides and worked examples for software applications in structural and molecular biology - from Yale Univ. - Offers more than 30 online services for DNA and protein bioinformatics analysis. - DBD is a database of predicted transcription factors in completely sequenced genomes. The predicted transcription factors all contain assignments to sequence specific DNA-binding domain families. - Provides an internet service that calculates the site, geometry and energy of small molecules interacting with proteins. - Online service integrating biological data from genomics, biochemistry, genetics and high-throughput expression profiling, to achieve a pattern-based analysis of genes and genomes. - Retrieves molecular biology data and bibliographic citations from the NCBI's integrated databases. - Consolidates evidence for gene-gene interactions from HPRD, BIND, Reactome, KEGG, GO, microarray co-expression and Y2H experiments. - Provides a complete set of bioinformatics tools and public databanks updated daily, and a range of links to seminars, training courses and platform news. - Web application that searches gene symbols or MeSH terms and displays resulting pairs of genes and MeSH terms that match the search term. - This platform provides over 100 methods for the analysis and visualization of gene expression, copy number, proteomic and other data. It enables biologists to add new analyses and create workflows that can be shared, edited and published. - Online version of the program for populational genetics. - GeneBio provides proteomics software tools and databases including SWISS-PROT, PROSITE, SWISS-2DPAGE and Melanie. We also offer a secure version of ExPASy molecular biology web server. - Several genomics and proteomics tools, including multiple alignments, gene expression analysis, tandem repeat and motif discovery. - Hosts Irish embnet node, Gives links to Database browsing and interrogation at SRS, European (EBI) servers, Blast server for parasite genomes (EBI), US (NCBI) servers, Protein structure prediction, PredictProtein Server in Heidelberg, Gene identification, splice sites, exons, introns and a list of gene structure prediction programs - The PubMed search system provides access to the MEDLINE and PREMEDLINE databases. - Online services including T-Coffee, El-Nemo, Casper and FeeBack. - A suite of online tools for analysis of DNA/RNA, proteins and arrays. - LGICdb is a curated repository of genes coding for subunits of Ligand-Gated Ion Channels. - A commercial service for improving the read length and quality of ABI 3730, 3130 and 3100 DNA sequencing traces. Works via reprocessing of the raw peak data before re-base calling. A free trial is provided. - MGRC provides contract genomes services, sequencing services, data and access services. - Web application that searches biological substances or MeSH terms and displays resulting pairs of substances and MeSH terms that match the search term. - MiMi Web provides an interface to a NCIBI data repository for conducting systems biology analyses. This repository includes the MiMI database, PubMed resources updated nightly, and text mined from biomedical research sources. - Framework and web portal specifically designed for the integration of bioinformatics software and databanks. Provides a tutorial and an interactive guided tour. - Information methodologies, tools, and technologies relating to the study of gene expression and signal transduction from the Institute for Transcriptional Informatics. - MINT is a database designed to store functional interactions between biological molecules (proteins, RNA, DNA). - Performs single-coverage local multiple DNA sequence alignments of finished and draft-quality genome sequences. It also provides with an option to predict transcription factor binding sites evolutionarily conserved across multiple species. - Protein ANnotation Diagram ORiented Analysis service that extracts biological information from user supplied sequences. - Service using the ParAlign algorithm to compare genetic sequences. Apparently it is as fast as BLAST and as sensitive as Smith-Waterman. - An integrated software system for storing, managing, analyzing, and querying metabolic pathways at genetic, molecular, biochemical and organism levels. - An online service for periodically performing predefined searches at NCBI, reporting new results by email or on the web. - Text and similarity searching, provided by the National Center for Biotechnology Information (NCBI). - Collection of sequence analysis tools. - Suite of user-friendly tools that evaluate the impact of gene splicing variation on specific molecular biology techniques. - Tool for querying Evidence Viewer Database (EVDB), a comprehensive, non-redundant collection of splice variant data for human genes. - Open web platform for modeling and reverse engineering of photosynthetic dynamism. - Scans sequences for potential transcription factor binding sites using JASPAR and TRANSFAC. - Interactive database of mRNA regions and motifs from all species and genomes. Users can browse the pre-computed data tables, search the sequence databases or search their own sequences. - A suite of tools for the analysis of sRNA datasets from high-throughput sequencing experiments. - A database of sequence comparisons between all publicly available prokaryotic genome sequences, allowing the on-line visualisation of comparisons between up to five genomic sequences, using the Artemis Comparison Tool. User can perform their comparisons on their own data. - Finds novel transcription factor binding sites by searching for over-represented (most significant motifs) motifs in DNA sequences. - A free web-based Laboratory Information Management System (LIMS), aimed at a typical small molecular biology laboratory allowing members to have their own private forum, events, Electronic Lab Notebook (ELN) and a LIMS area. - Helps users design zinc finger transcription factors. - Converts gp files from NCBI GenPept format to fasta. Its main purpose is to create fasta files with short, but still accurate headers for sequence. - Uses the network of genes and proteins as a natural way of accessing the millions of biomedical abstracts in PubMed.
