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> Ecological Databases
> Genome Databases
> Homology Detection
> Protein Analysis

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AG BIODV Software

Links to software developed by the AG BIODV group. Tools for consensus, alignment and definition. Both downloadable and Web-based.
(http://www.gsf.de/biodv/software.html)

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.
(http://www.biogis.huji.ac.il/)

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)

Biomolecular Interaction Network Database (BIND)

BIND is a database designed to store full descriptions of interactions, molecular complexes and pathways.
(http://bind.ca)

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.
(http://www.bionavigator.com/)

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)

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.
(http://cubic.bioc.columbia.edu/)

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/)

Entrez Browser

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

Fasta3

Sequence similarity and homology searching against nucleotide and protein database using the Fasta3 programs.
(http://www.ebi.ac.uk/fasta33/)

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).
(http://www.imtech.res.in/raghava/ftg/)

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)

Genepop on the Web

Online version of the program for populational genetics.
(http://wbiomed.curtin.edu.au/genepop/)

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)

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/)

GenomeNet WWW server

Very nice collection of bioinformatics tools, including BLAST and MOTIF - from Kyoto Univ.
(http://www.genome.ad.jp)

genomesapiens.org

presents the HIGH database, a curated annotation of human DNA regions that are proven to code for Immunoglobulin-superfamily proteins.
(http://www.genomesapiens.org/)

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
(http://acer.gen.tcd.ie/)

JustBio: Online Tool Set

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

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.
(http://www.matrixscience.com/cgi/index.pl?page=/search_form_)

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/filters.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.ch/melanie/)

Microarray Database Gateway

Tools for managing, accessing, and analyzing cDNA microarray data generated by the NCI Div. of Clinical Sciences ÂµArray Center - from the BioInformatics and Molecular Analysis Section of the NIH Center for Info. Technology.
(http://nciarray.nci.nih.gov)

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.
(http://transfac.gbf.de/)

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/)

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/)

NEBcutter V1.0

On-line DNA sequence tool to find large, non-overlapping, open reading frames and sites for all restriction enzymes-from New England BioLabs.
(http://tools.neb.com/NEBcutter/index.php3)

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.
(http://bimas.dcrt.nih.gov)

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/)

PEDANT

Completely automatic and exhaustive analysis of protein sequence sets - from individual sequences to complete genomes
(http://pedant.gsf.de/)

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)

ProPred

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.
(http://www.imtech.res.in/raghava/propred/)

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/)

REBASE

The restriction enzyme database, from New England Biolabs.
(http://rebase.neb.com/rebase/rebase.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. Research in Sequence Tag Alignment and Consensus Knowledgebase (STACK). Databases include BLAST search in Mycobacterium genome.
(http://www.sanbi.ac.za/)

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/)

Searching GenBank

Text and similarity searching, provided by the National Center for Biotechnology Information (NCBI).
(http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html)

Sequence Analysis (Bielefeld University Bioinformatics Server)

Collection of sequence analysis tools.
(http://bibiserv.techfak.uni-bielefeld.de/intro/seqdept.html)

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.
(http://stash.mrc-lmb.cam.ac.uk/SUPERFAMILY)

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/)

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/)

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://transfac.gbf.de/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.
(http://uther.otago.ac.nz/Transterm.html)

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/)

Virtual Genome Center

Online computational resources for PCR primer selection, similarity searching- from the Univ. of Minnesota.
(http://alces.med.umn.edu/VGC.html)

Webcutter 2.0

Free, online software for restriction mapping nucleotide sequences-from Yale Univ.
(http://www.firstmarket.com/cutter/cut2.html)

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