3D-PSSM
Fast, Web-based Method for Protein Fold Recognition using 1D and 3D Sequence Profiles coupled with Secondary Structure and Solvation Potential Information
A9 Search engine results
aMAZE
Database for the representation of information on networks of cellular processes: genetic regulation, biochemical pathways, signal transductions.
Amino Acid Structures
Array Genetics
Online bioinformatics products
Atelier BioInformatique
AZGeNetScene Visualizer
Navigate genetic regulatory pathway relations that are automatically extracted from biomedical literature
BAMBE
Bayesian Analysis in Molecular Biology and Evolution
Basic Blast 2.0
Basic GeneBee ClustalW 1.83
BestPrimers
BestPrimers(c) provides a simple interface for primers calculation, with FoldIndex(c) support.
Bielefeld University bioinformatics server
Genome Comparison, Alignments, Primer Design, RNA Studio, Evolutionary Relationships and Others
BioBike / BioLingua
Reducing the distance between biologists and biocomputation by providing an integrated, on-line, programmable biological knowledge base
Bioinformatics links
BioMail
New references from MEDLINE to your email account
Biomolecular research tools index
BioQuery
Provides a single, powerful user interface for building search strategies for different biomedical databases
BioWarehouse
Integrate multiple public bioinformatics databases into a single relational database system.
Blitz
Dedicated database searching service offered by the EBI which uses two different methods. Namely, MPsrch and Scanps
BRaunschweig ENzyme DAtabase (Brenda)
BRENDA (BRaunschweig ENzyme DAtabase) represents a comprehensive collection of enzyme and metabolic information, based on primary literature
Calculations | pactical molecular biology
Helps with basic molecular biological mathematics
CalPred
EF-hand calcium binding protein prediction and calcium binding region identification
CATH Protein Structure Classification
Hierarchical classification system for protein structures: it allows you to identify different structural classes by means of unique numbers and descriptive names
CBS Prediction Servers
Cell Cycle Ontology
An ontology for describing the cell cycle process
Clinical & Patient Aspects Databases
A meta database of links to Clinical & Patient Aspects Databases
Cn3D
View 3-dimensional structures from NCBI's Entrez retrieval service
CODEHOP
COnsensus-DEgenerate Hybrid Oligonucleotide Primers
Codon usage database
CPHmodels 2.0 Server
Homology modeling server
cybionix
bioinformatics hub
Darwin
Data Analysis and Retrieval With Indexed Nucleotide/peptide sequences
Databases and Tools for 3-D Protein Structure Comparison and Alignment
Using the Combinatorial Extension (CE) Method
DbBrowser
Provides facilities for interrogating the PRINTS database and a variety of other bio-databanks
DBGET Search - Protein-today
Web of Molecular Biology Databases
DNA Baser - DNA sequence assembly
Affordable alternative to the expensive DNA sequencing software on the market
DNA Data Bank of Japan (DDBJ)
Functioning as the international nucleotide sequence database.
EBI Genetic Code Viewer
EBI Tools: ClustalW
general purpose multiple sequence alignment program for DNA or proteins
EBI Tools: WU-Blast2
Washington University Basic Local Alignment Search Tool Version 2.0
eBioinformatics
Bioinformatics tools for MacOSX
EMBL Dali
Email server for 3-D protein structure database searches
EMBL in XML
Display data from the EMBL Nucleotide Sequence Database in XML formats, BSML and AGAVE.
EMBL WWW Gateway to AGADIR Service
An algorithm to predict the helical content of peptides
EMBL-ALIGN Information for Submitters
Emboss
package of free, Open Source software for molecular biology
Entrez cross-database search
Entrez Protein
The protein entries in the Entrez search and retrieval system have been compiled from a variety of sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq.
Eplore any 3D macromolecular structure model
Protein Explorer in Chime, FirstGlance in Jmol
ExPASy - Biochemical Pathways
Expert Protein Analysis System
Proteomics server of the Swiss Institute of Bioinformatics dedicated to the analysis of protein sequences and structures as well as 2-D PAGE.
FASTA email server
FirstGlance in Jmol
Macromolecular visualization with exceptional ease of use.
FoldIndex
Will this protein fold? This dynamic interactive process estimates the local and general probability
Genecards
GeneCards
GeneCards is an integrated database of human genes that includes automatically-mined genomic, proteomic and transcriptomic information.
GeneFisher
Interactive PCR Primer Design
GeneSifter
Microarray analysis: makes it easier to understand the biological significance of your microarray data using the latest annotation and statistics
GenomeNet
Bioinformatics center, institute for chemical research @ Kyoto University
GenomeQuest
Self-updating, reliable and secure genomic search solution that integrates biological sequence search capabilities, analytics, and patent content
GenoWiz
Microarray analysis: store, process and visualize gene expression data
GOBASE - The Organelle Genome Database
GOBASE is a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts.
Graphical Codon Usage Analyzer
Homeobox Genes DataBase
structural and functional genomics of hox ensembles
HTS Tools
High Throughput Screening (HTS) analysis
IDconverter
Map your ids to other known public DBs
Integr8 : Access to complete genomes and proteomes
The Integr8 web portal provides easy access to integrated information about deciphered genomes and their corresponding proteomes.
Intermine
General-purpose object-oriented data warehouse system developed as part of the FlyMine project
Jena library of biological macromolecules
Atlas of Macromolecule Structures
JWS Online - Online Cellular Systems Modelling
Simulation of kinetic models from a curated model database
KegTools
KegHier, KegArray and KegDraw
Labbook
LabBook and BSML Technology
Malaria parasite
Metabolic pathways
Malaysian Genomics Resource Centre
Free online bioinformatics tools
MAPPER
platform for the computational identification of transcription factor binding sites (TFBSs) in multiple genomes.
Match-Box Web Server
Protein sequence multiple alignment tools based on strict statistical criteria
MDL Chemscape en MDL Chime
MetaCyc
Multiorganism database of metabolic pathways and enzymes.
MetNet project
The MetNet project for analyzing experimental data in the context of metabolic and regulatory networks
Mfold Server
RNA and DNA folding package
Molecules to go
NCBI Blast
NetNGlyc 1.0 Server
NetPrimer
Nucleic acid sequence analysis
Six-frame sequence translation, Fast sequence identity search
Nucleic Acid to Amino Acid Translation
OCA Bowser-Database for Structure and Fucntion
OCA facilitates the understanding of the genomics/proteomics biological data through data analysis and synthesis.
OMIM - Online Mendelian Inheritance in Man
Catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere [NCBI]
Online DNA interaction
Manipulate and Display a DNA Sequence
OWL BLAST Server
PaLS: Pathway and Literature Strainer
Filtering of genes/proteins according to their shared information
PathArt
Pathway Articulator by Jubilant Biosys
Pathway Tools
Genome-scale manipulation of metabolic pathways and transcriptional regulatory networks.
Patika
Pathway Analysis Tools for Integration and Knowledge Acquisition
PatScan
Pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern
PCR box titration calculator
PDB Records Name
Distribution of Records in PDB files (indispensable for extracting data from multiple PDB files)
PDB retriever
PDB2MGIF
Converts PDB protein structures to animated GIFs
Pedant3: Munich information center for protein sequences
Pre-computed analyses to analyse protein function: Blast similarity searches against non-redundant protein sequence database, motif searches against the Pfam, BLOCKS and PROSITE databases
Pfam
large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families
PIMRider
Protein Interaction Map - Hybrigenics
PISE
A tool to generate Web interfaces for Molecular Biology programs
PPSearch - Protein motifs Search
Dearch your query sequence for protein motifs, rapidly compare your query protein sequence against all patterns stored in the PROSITE pattern database
Pratt
Pattern Matching
PredictProtein
Service for sequence analysis, structure and function prediction
Primer3
Pick primers from a DNA sequence
Pro-3D
Three-Dimensional Protein Analysis Program
ProcessDB
ProcessDB
Prosite
Database of protein domains, families and functional sites
Protein Explorer
Macromolecular visualization with help for beginners and power for specialists. Creates MolSlides.
Protein Similarity Search
PROWL
Laboratory of Mass Spectrometry and Gaseous Ion Chemistry
PSort
Prediction of protein localization sites in cells
PubGene
Retrieve information on genes and proteins. The underlying structure of PubGene can be viewed as a "gene-centric" database
Puzzle
Tree reconstruction for sequences by quartet puzzling and maximum likelihood
PyMOL
Molecular visualization system on an OPEN-SOURCE foundation
RasMol
Molecular Graphics Visualisation Tool
RCSB PDB
Research collaboratory for structural bioinformatics: tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease
Readseq
Online biosequence conversion tool
RecentReferences
RecentReferences will try to find recent publications related to your sequence.
Relibase
Protein-ligand database query tool
REMAP
Display a sequence with restriction cut sites, translation etc...
Retroviruses
Collection of resources at NCBI specifically designed to support the research of retroviruses
RiboClub
Website with RNA related bioingformatic tools
SAM - Sequence Alignment and Modeling System
Flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis.
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
SeqFacts
A tool for sequence identification, analysis, characterization and annotation. This server will try to find relevant information related to your sequence.
SeqPup
Biological sequence editor and analysis program
Sequence analysis tools interfaced at the Pasteur Institute
SeWER
SEquence analysis using WEb Resources
Sight
Automatic running of bioinformatical tools on remote servers
SignalP 3.0 server
SMD - Stanford Microarray Database
SSAHA2: Sequence Search and Alignment by Hashing Algorithm
Very fast DNA alignment tool
SSCP - Secondary Structural Content Prediction
Computes predictions for the content of helix, strand, and coil for a given protein using the amino acid composition as the only input information
Structural Classification of Proteins
SuggestES
Suggest an Expression System based on a provided sequence. suggestES takes the protein sequence you provide and scans a large database with protein sequences with known results for different expression systems.
Swiss-Prot Protein knowledgebase
The UniProt Knowledgebase consists of UniProtKB/Swiss-Prot and UniProtKB/TrEMBL.
Swiss-Shop
Obtain new protein sequence entries (UniProtKB/Swiss-Prot) relevant to your interest.
The NCBI Taxonomy Homepage
This database provides taxonomic information about organisms
TIGR
The Institute for Genome Research
TraceSearch
Search the whole WTSI trace archive by sequence similarity
Translate tool
Translate is a tool which allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence.
Trypanosoma cruzi Blast Search
VigyaanCD
Electronic workbench for bioinformatics, computational biology and computational chemistry [based on Knoppix Linux]
VisANT - Predictome
Integrative Visual Analysis Tool for Biological Networks and Pathways
VSNS Biocomputing division
Web Primer: DNA and Purpose Entry
Webcutter
World Index of Molecular Visualization Resources
User-maintained indices of links to 3D molecular structural resources.
WU-Blast2 - Parasite Genomes Database Query
his tool is specifically designed to blast sequences against parasite genomes.
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