Online Services - Twitter Search

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johnlocke185 (John Locke) Tue, 15 Dec 2009 07:06:05 -0000
Russia top online services http://www.associatedcontent.com/article/2480404/top_online_russia_news_services.html?cat=9
Russia top online services http://www.associatedcontent.com/article/2480404/top_online_russia_news_services.html?cat=9
pbfedorov (Pavel Fedorov) Tue, 15 Dec 2009 07:05:36 -0000
Russia top online services http://www.associatedcontent.com/article/2480404/top_online_russia_news_services.html?cat=9
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Franksterville (Franksterville) Tue, 15 Dec 2009 06:57:08 -0000
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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.

Content - Several genomics and proteomics tools, including multiple alignments, gene expression analysis, tandem repeat and motif discovery.

Advanced Genetics Wizard - Online program that calculates the distribution of offspring genotypes from dominant, codominant and recessive gene crosses, for up to 6 genes.
Meta Description: [ Advanced Genetics Wizard is a free, online program that calculates the genetic makeup of offspring from dominant, codominant and recessive gene crosses. ]

Ascidian Network - An online database able to relate expression data with other data such as lineage, induction, cell fates, genomic information, blastomere position and morphology in the developing ascidian embryo.

Bacterial Identification - Service for the identification of bacteria and fungi sequences by sequence alignment.

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 regulatory DNA sequences and protein factors binding to and acting through them.

BioModels Database - 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.
Meta Description: [ BioMolecular Engineering Research Center, specializing in Bioinformatics research, protein functional profiles, protein structure prediction, genome analysis and visualisations, and promoter analysis. ]

Biomolecular Interaction Network Database (BIND) - BIND is a database designed to store full descriptions of interactions, molecular complexes and pathways.

Bioverse - Provides a framework for exploring the relationships among the molecular, genomic, proteomic, systems, and organismal worlds.

500 Canadian Bioinformatics Help Desk - We provide bioinformatics support, services, servers, and software to Canadian researchers.

500 CAP Sequence Assembler - DNA sequence assembly and contig formation.

Carnac - 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.
Meta Description: [ User Guides and worked examples for software applications in structural biology ]

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 protein structure prediction servers, and DSSPcont for continuous assignment of protein secondary structure.
Meta Description: [ Columbia University Bioinformatics Center ]

ERGO - Online service integrating biological data from genomics, biochemistry, genetics and high-throughput expression profiling, to achieve a comprehensive pattern-based analysis of genes and genomes.

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.

Gene and Protein Synonyms DataBase - Free service for retrieving all synonyms for a given gene or protein name.
Meta Description: [ Text mining for biomedical literature - A free text mining application for the biomedical community. ]

Gene Expression Data Analysis - Normalization tests for differentially expressed genes, clustering, bootstrapping, leave-one-out validation, cross-fold validation.
Meta Description: [ Online Gene Expression Data Simulator and Analysis tool. ]

500 Gene Network Reconstruction - Reconstruction of gene regulatory networks from time-series microarray expression data sets.

Genepop on the Web - Online version of the program for populational genetics.

404 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

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.
Meta Description: [ Proteomics software for the life science community with a focus on protein identification and characterization as well as proteome imaging. ]

500 GenomeSURF - Colorful visualization of Sequence Frequency. Includes Human and Mouse Genomic Sequences. Evaluate uniqueness of graphically.

iHOP - Uses the network of genes and proteins as a natural way of accessing the millions of biomedical abstracts in PubMed.
Meta Description: [ iHOP - Information Hyperlinked over Proteins. iHOP provides the network of genes and proteins as a natural way of accessing the millions of abstracts in PubMed. By employing genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed becomes bound together into one... ]

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

Information Génomique et Structurale (CNRS) - Online services including T-Coffee, El-Nemo, Casper and FeeBack.
Meta Description: [ IGS homepage ]

InstaSeq - Google-based search engine for DNA, RNA or Protein sequences.
Meta Description: [ A Google powered bioinformatics search tool to mine the web for biological sequences and related records ]

JustBio: Online Tool Set - A Suite of Online tools for analysis of DNA/RNA, Proteins, and Arrays.

500 Kangaroo - Search for motifs and paterns within amino acid and nucleotide databases

Ligand-Gated Ion Channel Database - LGICdb is a curated repository of genes coding for subunits of Ligand-Gated Ion Channels.
Meta Description: [ European Bioinformatics Institute - Computational Neurobiology ]

MedMiner - An Internet biomedical data-mining tool for organizing search information gathered from textual or genetic databases - from the NIH National Cancer Inst.

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.

Molecular Interactions Database (MINT) - MINT is a database designed to store functional interactions between biological molecules (proteins, RNA, DNA).

Mulan - 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.

My Genomics Resource Centre - A Malaysian Genomics toolset for high-throughput analysis of biological data. Must register to use.

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.

PANDORA - Protein ANnotation Diagram ORiented Analysis service that extracts biological information from user supplied sequences.
Meta Description: [ PANDORA offers biological annotation-based analysis of protein sets. Integration of annotation sources and intersection-inclusion DAG allow meaningful biological interpretation. keywords: proteins bioinformatics annotations proteomics computational molecular biology ]

ParAlign - Service using the ParAlign algorithm to compare genetic sequences. Apparently it is as fast as BLAST and as sensitive as Smith-Waterman.
Meta Description: [ Rapid and sensitive sequence similarity searches powered by parallel computing technology ]

PEDANT - Completely automatic and exhaustive analysis of protein sequence sets - from individual sequences to complete genomes
Meta Description: [ IBI, mips, Bioinformatics ]

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.

PlasMapper - Online service to generate annotated plasmid maps up to 20 kbp. Outputs in PNG, JPG, SVG or SVGZ format.

ProPred-I - An online service for predicting MHC binding regions in antigens. It also offers the proteasomal and immunoproteasomal filters to improve the applicability of results.
Meta Description: [ The ProPred-I is a web server for predicting MHC class binding peptides. It predicts the promiscuous peptides ]

ProteinLounge - Bioinformatics portal which integrates protein information and many databases and research tools useful for researchers and students. Subscription based service.

PubCrawler - An online service for periodically performing predefined searches at NCBI, reporting new results by email or on the web.
Meta Description: [ PubCrawler - a free Update AlertingService for PubMed and GenBank (Home Page) ]

ReadSeq - Converts amino acid and nucleotide sequence data formats including FASTA, GenBank, Phylip and others.

404 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.

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.

Sequence Analysis (Bielefeld University Bioinformatics Server) - Collection of sequence analysis tools.

Simulation programs for teaching population dynamics - Offers a number of educational programs including LESLIE, LOGIST, CHAOS, CELLS, WITCOM, PRED and LEWONTIN.
Meta Description: [ Web-based educational computer simulation programs can be started from this page. In our population dynamics course we use the following programs: LESLIE, LOGIST, CHAOS, CELLS, WITCOM, PRED and LEWONTIN ]

Systems Biology of Photosynthesis - Open web platform for modeling and reverse engineering of photosynthetic dynamism.
Meta Description: [ Systems biology of photosynthesis in dynamic light environment. Open web platform for modeling and reverse engineering of photosynthetic dynamism. ]

TFM Explorer - Scans sequences for potential Transcription Factor binding sites using Patser and TRANSFAC.

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.

404 Virtual Genome Center - Online computational resources for PCR primer selection, similarity searching- from the Univ. of Minnesota.

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 by Fast Fourier Transform), and biological databases.

WebACT - 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.