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
AG BIODV Software -
Links to software developed by the AG BIODV group. Tools for consensus,
alignment and definition. Both downloadable and Web-based.
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.
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.
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.
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
Entrez Browser - Retrieves
molecular biology data and bibliographic citations from the NCBI's integrated
databases.
Fasta3 - Sequence similarity and
homology searching against nucleotide and protein database using the Fasta3
programs.
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.
Genepop on the Web -
Online version of the program for populational genetics.
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.
GenomeNet WWW server - Very nice
collection of bioinformatics tools, including BLAST and MOTIF - from Kyoto Univ.
genomesapiens.org - presents the
HIGH database, a curated annotation of human DNA regions that are proven to code
for Immunoglobulin-superfamily proteins.
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
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.
MedMiner -
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
- Powerful, state-of-the-art, 2-D analysis software package with user-friendly
interface from the Swiss Institute of Bioinformatics (SIB).
MendelBase
- MendelBase is a database of functional and structural/biophysical information
pertaining to proteins. Run by Array Genetics. [Registration required]
Metalife Database - Offers a
searchable database of proteins and other organic materials.
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.
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.
Multiple Sequence
Alignment - Online services for multiple sequence alignment, including
ctree, clustalw and msa. Includes sources to build clustalw on your system.
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.
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.
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.
PEDANT - Completely
automatic and exhaustive analysis of protein sequence sets - from individual
sequences to complete genomes
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.
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.
RNAGENiE - An online program which
locates novel RNA genes in genomic DNA.
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.
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.
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.
Virtual Genome Center -
Online computational resources for PCR primer selection, similarity searching-
from the Univ. of Minnesota.
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.
