Biology: Bioinformatics: Online Services

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Ecological Databases (0)

Gene Expression and Regulation (6)

Genome Databases (7)

Homology Detection (11)

Molecular Biology Tools (3)

Phylogenetic Analysis (8)

Protein Analysis (22)

LINKS:

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BIOBASE
http://www.gene-regulation.com/
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.

BioGIS: Israel Biodiversity Information System
http://www.biogis.huji.ac.il/
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.

BioMolecular Engineering Research Center
http://bmerc-www.bu.edu/index.html
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)
http://bind.ca
BIND is a database designed to store full descriptions of interactions, molecular complexes and pathways.

CAP Sequence Assembler
http://bio.ifom-firc.it/ASSEMBLY/assemble.html
DNA sequence assembly and contig formation.

Carbohydrate-Active Enzymes (CAZy) database
http://afmb.cnrs-mrs.fr/CAZY/
Describes the families of structurally-related catalytic and carbohydrate-binding functional domains of enzymes that degrade, modify, or create glycosidic bonds.

Center Structural Biology: Programs and Tools
http://www.csb.yale.edu
User guides and worked examples for software applications in structural and molecular biology - from Yale Univ.

CUBIC: Columbia University Bioinformatics Center
http://cubic.bioc.columbia.edu/
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.

Database of Interacting Proteins (DIP)
http://dip.doe-mbi.ucla.edu/
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.

Entrez Browser
http://www.ncbi.nlm.nih.gov/Entrez/
Retrieves molecular biology data and bibliographic citations from the NCBI's integrated databases.

FIE (5' end Information Extraction)
http://sdmc.lit.org.sg/FIE/
Gene sequence extraction of regions around the 5'-end (promoter) and/or the translation initiation site (TIS) of a gene.

GeneCards: Human Genes, Proteins, and Diseases
http://nciarray.nci.nih.gov/cards/index.html
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.

Genepop on the Web
http://wbiomed.curtin.edu.au/genepop/
Online version of the program for populational genetics.

General Repository for Interaction Datasets (GRID)
http://biodata.mshri.on.ca/grid/servlet/Index
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.
http://www.genebio.com/
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.

GenomeSURF
http://surf.gi.k.u-tokyo.ac.jp
Colorful visualization of Sequence Frequency. Includes Human and Mouse Genomic Sequences. Evaluate uniqueness of graphically.

IBM Bioinformatics Group - Tools & Content
http://cbcsrv.watson.ibm.com/Tspd.html
Several genomics and proteomics tools, including multiple alignments, gene expression analysis, tandem repeat and motif discovery.

INCBI Irish National Centre for BioInformatics
http://acer.gen.tcd.ie/
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

JustBio: Online Tool Set
http://www.justbio.com
A Suite of Online tools for analysis of DNA/RNA, Proteins, and Arrays.

Kangaroo
http://www.blueprint.org/products/kangaroo/kangaroo_search.html
Search for motifs and paterns within amino acid and nucleotide databases

MedMiner
http://discover.nci.nih.gov/textmining/main.jsp
An Internet biomedical data-mining tool for organizing search information gathered from textual or genetic databases - from the NIH National Cancer Inst.

Melanie II 2-D Analysis Software
http://www.expasy.org/melanie/
Powerful, state-of-the-art, 2-D analysis software package with user-friendly interface from the Swiss Institute of Bioinformatics (SIB).

Molecular Informatics Resource for the Analysis of Gene Expression
http://www.ifti.org/
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)
http://cbm.bio.uniroma2.it/mint/
MINT is a database designed to store functional interactions between biological molecules (proteins, RNA, DNA).

NIH BioInformatics and Molecular Analysis Section
http://bimas.dcrt.nih.gov
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.

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