Online Services (Bioinformatics)

Online Services Subs:

Directories@ Ecological Databases Gene Expression and Regulation Genome Databases Homology Detection

Homology Detection Molecular Biology Tools Phylogenetic Analysis Protein Analysis Software@

Online Services Sites:

BIOBASE 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 regulato http://www.gene-regulation.com/ Protein Structure Prediction Using Web Resources SPORes is a website for protein structure prediction using the web browser as an interface to software that runs of web servers or other resources available over the world wide web. http://cgat.ukm.my/spores/ TRANSFAC-The Transcription Factor Database Very thorough compilation of transcriptional regulatory protein factors & their cognate gene promoter elements along with DNA sequence search & analysis programs - from GBF, Braunschweig, Germany. http://www.gene-regulation.com/pub/databases.html#transfac PIR-International Protein Sequence Database produces a comprehensive, non-redundant, and expertly annotated protein sequence database. PIR features integrated annotation search to support functional/structural genomics and proteomic research. http://pir.georgetown.edu 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. http://www.cs.ucr.edu/~stelo/Verbumculus/ Scansite Scansite searches for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains. http://scansite.mit.edu/ YMF - DNA Motif Finding Program Finds novel transcription factor binding sites by searching for over-represented (most significant motifs) motifs in DNA sequences. http://abstract.cs.washington.edu/~saurabh/YMFWeb/YMFInput.pl PEDANT Completely automatic and exhaustive analysis of protein sequence sets - from individual sequences to complete genomes http://pedant.gsf.de/ CUBIC: Columbia University Bioinformatics Center Features PredictProtein service for sequence analysis and protein structure prediction, META for single-page interface to validated sequence analysis, PredictNLS for prediction and analysis of nuclear localization signals, EVA for evaluation of automatic http://cubic.bioc.columbia.edu/ Transterm - a database of mRNA regions and motifs Transterm - an 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. http://uther.otago.ac.nz/Transterm.html Database of Interacting Proteins (DIP) The DIP catalogs experimentally determined interactions between proteins while combining information from a variety of sources to create a single, consistent set of protein-protein interactions. http://dip.doe-mbi.ucla.edu/ FIE (5' end Information Extraction) Gene sequence extraction of regions around the 5'-end (promoter) and/or the translation initiation site (TIS) of a gene. http://sdmc.lit.org.sg/FIE/ Online Lab Reporting A service that allows clinical laboratories to send test results to referring physicians over the internet. A help forum and FAQ pages are included. http://www.labreporting.com/ Kangaroo Search for motifs and paterns within amino acid and nucleotide databases http://www.blueprint.org/products/kangaroo/kangaroo_search.html General Repository for Interaction Datasets (GRID) The GRID is a database of genetic and physical interactions. It contains interaction data from many sources, including several genome/proteome-wide studies, the MIPS database, and BIND http://biodata.mshri.on.ca/grid/servlet/Index ProteinLounge Bioinformatics portal which integrates protein information and many databases and research tools useful for researchers and students. Subscription based service. http://www.proteinlounge.com 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. http://bmerc-www.bu.edu/index.html Carbohydrate-Active Enzymes (CAZy) database Describes the families of structurally-related catalytic and carbohydrate-binding functional domains of enzymes that degrade, modify, or create glycosidic bonds. http://afmb.cnrs-mrs.fr/CAZY/ ReadSeq Convert various aminoacid and nucleotide sequence data formats including FASTA, GenBank, Phylip and others. http://bimas.dcrt.nih.gov/molbio/readseq/ 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. http://www.genebio.com/ 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. http://www.ifti.org/ MedMiner An Internet biomedical data-mining tool for organizing search information gathered from textual or genetic databases - from the NIH National Cancer Inst. http://discover.nci.nih.gov/textmining/main.jsp GeneCards: Human Genes, Proteins, and Diseases Database of concise information about human genes (and their mouse homologs), focusing on their cellular functions and medical aspects - from the Weizmann Inst. of Science. http://nciarray.nci.nih.gov/cards/index.html SA National Bioinformatics Institute SANBI aims to bring genome information, computational biology, and analytical tools to the South African research community. Hosts SA National EMBNet Node, provides links to Sequence Retrieval System (SRS), GeneKraal, and TB Genomes Analysis Server. Resea http://www.sanbi.ac.za/ Genepop on the Web Online version of the program for populational genetics. http://wbiomed.curtin.edu.au/genepop/ NIH BioInformatics and Molecular Analysis Section Numerous computational tools and resources to unite advances in biology with those in computers, informatics, and networking for the genomic and genetic analysis fields of BioInformatics; division of the Computational Bioscience and Engineering Lab at the http://bimas.dcrt.nih.gov IBM Bioinformatics Group - Tools & Content Several genomics and proteomics tools, including multiple alignments, gene expression analysis, tandem repeat and motif discovery. http://cbcsrv.watson.ibm.com/Tspd.html 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, http://acer.gen.tcd.ie/ Sequence Analysis (Bielefeld University Bioinformatics Server) Collection of sequence analysis tools. http://bibiserv.techfak.uni-bielefeld.de/intro/seqdept.html Center Structural Biology: Programs and Tools User guides and worked examples for software applications in structural and molecular biology - from Yale Univ. http://www.csb.yale.edu Entrez Browser Retrieves molecular biology data and bibliographic citations from the NCBI's integrated databases. http://www.ncbi.nlm.nih.gov/Entrez/ Biomolecular Interaction Network Database (BIND) BIND is a database designed to store full descriptions of interactions, molecular complexes and pathways. http://bind.ca The XEMBL Project XEMBL provides access to the EMBL/GenBank/DDBJ Nucleotide Sequence Database, providing output in various XML standards. http://www.ebi.ac.uk/xembl/ Searching GenBank Text and similarity searching, provided by the National Center for Biotechnology Information (NCBI). http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html Melanie II 2-D Analysis Software Powerful, state-of-the-art, 2-D analysis software package with user-friendly interface from the Swiss Institute of Bioinformatics (SIB). http://www.expasy.org/melanie/ Molecular Interactions Database (MINT) MINT is a database designed to store functional interactions between biological molecules (proteins, RNA, DNA). http://cbm.bio.uniroma2.it/mint/ Transcription Element Search Software (TESS) Very helpful software for locating and displaying transcription factor binding sites within DNA sequences - from the Univ. of Penn. http://www.cbil.upenn.edu/tess/ Virtual Genome Center Online computational resources for PCR primer selection, similarity searching- from the Univ. of Minnesota. http://alces.med.umn.edu/VGC.html JustBio: Online Tool Set A Suite of Online tools for analysis of DNA/RNA, Proteins, and Arrays. http://www.justbio.com BioGIS: Israel Biodiversity Information System Israel Biodiversity Information System (BioGIS) is a Geographical Information System established to create a national database of the flora and fauna of Israel. The system is open to the public and provides advanced tools for querying, analyzing, modeling http://www.biogis.huji.ac.il/ GenomeSURF Colorful visualization of Sequence Frequency. Includes Human and Mouse Genomic Sequences. Evaluate uniqueness of graphically. http://surf.gi.k.u-tokyo.ac.jp CAP Sequence Assembler DNA sequence assembly and contig formation. http://bio.ifom-firc.it/ASSEMBLY/assemble.html Web Services at Institute of Microbial Technology, Chandigarh, India Protein structure prediction (Protein Structural Classes, Secondary Structure Prediction), immunological methods (ProPred), genomics & proteomics (Genome Wise Sequence Similarity Search, Spectral Repeat Finder, 2D Gel Comparison, protein coding gene http://imtech.res.in/raghava/www.html

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