Online Services

Online Services

• Directories and Portals@
• Ecological Databases
• Genome Databases
• Homology Detection
• Protein Analysis
• Sites about Software@

Online Services Links

• 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.
  
  
• genomesapiens.org presents the HIGH database, a curated annotation of human DNA regions that are proven to code for Immunoglobulin-superfamily proteins.
  
• Genepop on the Web Online version of the program for populational genetics.
  
• Virtual Genome Center Online computational resources for PCR primer selection, similarity searching- from the Univ. of Minnesota.
  
• Matrix Science Mascot is an on-line search engine for protein identification using mass spectrometry data. Search NCBI nr and dbEST using peptide mass fingerprint data, sequence queries, and MS/MS peak lists.
  
• 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).
  
• RNAGENiE An online program which locates novel RNA genes in genomic DNA.
  
• FTG: Fast Fourier Transform approach for locating protein coding genes This site provides user a choice of using different Fourier Transform based techniques on their genomic sequences to identify protein coding regions in the genome. This algorithm improves the efficiency of gene prediction and does not require any learning set. (Unfortunately, uses client-side scripting which seems broken in IE 5.5).
  
• 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.
  
• 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.
  
• Sequence Analysis Software Several basic online software tools for DNA sequence analysis - from Attotron Biosensor Corp.
  
• Molecular Bioinformatics of Gene Regulation 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.
  
• 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.
  
• MedMiner An Internet biomedical data-mining tool for organizing search information gathered from textual or genetic databases - from the NIH National Cancer Inst.
  
• CUBIC: Columbia University Bioinformatics Center Services - PredictProtein for sequence analysis and protein structure prediction , META for single-page interface to validated sequence analysis, Links to WWW services for molecular biology, and analysing entire genomes
  
• A web Server for prediction of Promiscuous MHC binding regions This server allows the prediction of promiscuous MHC binding regions in an antigen, which are useful for subunit vaccine design. The 51 HLA DR alleles are used for prediction by the server.
  
• Entrez Browser Retrieves molecular biology data and bibliographic citations from the NCBI's integrated databases.
  
• MendelBase MendelBase is a database of functional and structural/biophysical information pertaining to proteins. Run by Array Genetics. [Registration required]
  
• Center Structural Biology: Programs and Tools User guides and worked examples for software applications in structural and molecular biology - from Yale Univ.
  
• The XEMBL Project XEMBL provides access to the EMBL/GenBank/DDBJ Nucleotide Sequence Database, providing output in various XML standards.
  
• GenomeNet WWW server Very nice collection of bioinformatics tools, including BLAST and MOTIF - from Kyoto Univ.
  
• Official REBASE Homepage The restriction enzyme database - from New England Biolabs.
  
• 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
  
• 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 Center for Information Technology.
  
• Searching GenBank Text and similarity searching, provided by the National Center for Biotechnology Information (NCBI).
  
• 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.
  
• Sequence Analysis (Bielefeld University Bioinformatics Server) Collection of sequence analysis tools.
  
• AG BIODV Software Links to software developed by the AG BIODV group. Tools for consensus, alignment and definition. Both downloadable and Web-based.
  
• 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.
  
• 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, and visualizing patterns of species distribution.
  
• SUPERFAMILY HMM library for Structural Assignments to protein sequences and Genomes This server is a Hidden Markov Model library providing 3 services: sequence searching, sequence alignments and genome assignments.
  
• 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.
  
• Microarray Database Gateway Tools for managing, accessing, and analyzing cDNA microarray data generated by the NCI Div. of Clinical Sciences µArray Center - from the BioInformatics and Molecular Analysis Section of the NIH Center for Info. Technology.
  
• 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.
  
• 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. Research in Sequence Tag Alignment and Consensus Knowledgebase (STACK). Databases include BLAST search in Mycobacterium genome.
  
• Bionavigator Provides an integrated set of online tools that allow use of GCG, BLAST and other programs. Also allows data storage. Commercial site with some free services.
  
• 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.
  
• Multiple Sequence Alignment Online services for multiple sequence alignment, including ctree, clustalw and msa. Includes sources to build clustalw on your system.