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Gene Expression and Regulation
Molecular Biology Tools
Science: Biology: Bioinformatics: Software
Transcription Element Search Software (TESS)
- Very helpful software for locating and displaying transcription factor binding sites within DNA sequences - from the Univ. of Penn.
Verbumculus Genetic Sequence Analyzer
- 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.
Advanced Genetics Wizard
- Online program that calculates the distribution of offspring genotypes from dominant, codominant and recessive gene crosses, for up to 6 genes.
- Service for the identification of bacteria and fungi sequences by sequence alignment.
- 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.
- 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.
BioMolecular Engineering Research Center
- 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.
Biomolecular Interaction Network Database (BIND)
- BIND is a database designed to store full descriptions of interactions, molecular complexes and pathways.
Broad Institute: Software
- 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.
- A free software tool for analysing the hypothetical secondary structure of a family of homologous RNA.
Center for Biological Sequence Analysis
- Offers more than 30 online services for DNA and protein bioinformatics analysis.
Center Structural Biology: Programs and Tools
- User guides and worked examples for software applications in structural and molecular biology - from Yale Univ.
- Provides an internet service that calculates the site, geometry and energy of small molecules interacting with proteins.
Functional Human Gene Network
- Consolidates evidence for gene-gene interactions from HPRD, BIND, Reactome, KEGG, GO, microarray co-expression and Y2H experiments.
- 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.
Genepop on the Web
- Online version of the program for populational genetics.
Geneva Bioinformatics (GeneBio) S.A.
- 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.
GenOuest Bioinformatics Platform
- Provides a complete set of bioinformatics tools and public databanks updated daily, and a range of links to seminars, training courses and platform news.
- 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.
INCBI Irish National Centre for BioInformatics
- 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
Informatics Tools in PubMed
- The PubMed search system provides access to the MEDLINE and PREMEDLINE databases.
JustBio: Online Tool Set
- A suite of online tools for analysis of DNA/RNA, proteins and arrays.
Ligand-Gated Ion Channel Database
- LGICdb is a curated repository of genes coding for subunits of Ligand-Gated Ion Channels.
LongTrace DNA Sequencing Service
- 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.
Malaysian Genomics Resource Centre Berhad
- 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.
Michigan Molecular Interactions
- 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.
Molecular Informatics Resource for the Analysis of Gene Expression
- Information methodologies, tools, and technologies relating to the study of gene expression and signal transduction from the Institute for Transcriptional Informatics.
- 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 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).
Systems Biology of Photosynthesis
- Open web platform for modeling and reverse engineering of photosynthetic dynamism.
- Scans sequences for potential transcription factor binding sites using JASPAR and TRANSFAC.
UEA Plant sRNA Toolkit
- 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.
YMF - DNA Motif Finding Program
- Finds novel transcription factor binding sites by searching for over-represented (most significant motifs) motifs in DNA sequences.
Zinc Finger Tools
- Helps users design zinc finger transcription factors.
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