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Web Sitesi

Carbohydrate-Active Enzymes (CAZy) database
Describes the families of structurally-related catalytic and carbohydrate-binding functional
domains of enzymes that degrade, modify, or create glycosidic bonds.

http://afmb.cnrs-mrs.fr/CAZY/
Reviews Rating: Not yet Rated Whois Check

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

http://www.proteinlounge.com
Reviews Rating: Not yet Rated Whois Check

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.

http://www.gene-regulation.com/
Reviews Rating: Not yet Rated Whois Check

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://www.gene-regulation.com/pub/databases.html#transfac
Reviews Rating: Not yet Rated Whois Check

CAP Sequence Assembler
DNA sequence assembly and contig formation.
http://bio.ifom-firc.it/ASSEMBLY/assemble.html
Reviews Rating: Not yet Rated Whois Check

Blocks WWW Server
Resources for biological sequence analysis, including conserved region homology,
consensus-degenerate PCR primer design and tutorial, at the Fred Hutchinson Cancer Research Center
in Seattle, WA.

http://www.blocks.fhcrc.org/
Reviews Rating: Not yet Rated Whois Check

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.

http://imtech.res.in/raghava/www.html
Reviews Rating: Not yet Rated Whois Check

Natural Killer Cell Receptor Database (NKCR DB)
A specialised database containing sequence data and other information on NK cell receptors.
http://www.bioinformatics.leeds.ac.uk/~bmbst/NKCR/home.php
Reviews Rating: Not yet Rated Whois Check

YMF - DNA Motif Finding Program
Finds novel transcription factor binding sites by searching for over-represented (most significant
motifs) motifs in DNA sequences.

http://abstract.cs.washington.edu/~saurabh/YMFWeb/YMFInput.pl
Reviews Rating: Not yet Rated Whois Check

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.

http://sdmc.lit.org.sg/FIE/
Reviews Rating: Not yet Rated Whois Check

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

http://surf.gi.k.u-tokyo.ac.jp
Reviews Rating: Not yet Rated Whois Check

Kangaroo
Search for motifs and paterns within amino acid and nucleotide databases
http://bioinfo.mshri.on.ca/kangaroo/kangaroo.html
Reviews Rating: Not yet Rated Whois Check

ReadSeq
Convert various aminoacid and nucleotide sequence data formats including FASTA, GenBank, Phylip and
others.

http://bimas.dcrt.nih.gov/molbio/readseq/
Reviews Rating: Not yet Rated Whois Check

IBM Bioinformatics Group - Tools & Content
Several genomics and proteomics tools, including multiple alignments, gene expression analysis,
tandem repeat and motif discovery.

http://cbcsrv.watson.ibm.com/Tspd.html
Reviews Rating: Not yet Rated Whois Check

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/
Reviews Rating: Not yet Rated Whois Check

JustBio: Online Tool Set
A Suite of Online tools for analysis of DNA/RNA, Proteins, and Arrays.
http://www.justbio.com
Reviews Rating: Not yet Rated Whois Check

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/
Reviews Rating: Not yet Rated Whois Check

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/
Reviews Rating: Not yet Rated Whois Check

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/
Reviews Rating: Not yet Rated Whois Check

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
Reviews Rating: Not yet Rated Whois Check

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/
Reviews Rating: Not yet Rated Whois Check

PEDANT
Completely automatic and exhaustive analysis of protein sequence sets - from individual sequences
to complete genomes

http://pedant.gsf.de/
Reviews Rating: Not yet Rated Whois Check

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

http://bind.ca
Reviews Rating: Not yet Rated Whois Check

Fasta3
Sequence similarity and homology searching against nucleotide and protein database using the Fasta3
programs.

http://www.ebi.ac.uk/fasta33/
Reviews Rating: Not yet Rated Whois Check

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
Reviews Rating: Not yet Rated Whois Check

GenomeNet WWW server
Very nice collection of bioinformatics tools, including BLAST and MOTIF - from Kyoto Univ.
http://www.genome.ad.jp
Reviews Rating: Not yet Rated Whois Check

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

http://alces.med.umn.edu/VGC.html
Reviews Rating: Not yet Rated Whois Check

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/
Reviews Rating: Not yet Rated Whois Check

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/
Reviews Rating: Not yet Rated Whois Check

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/
Reviews Rating: Not yet Rated Whois Check

Genepop on the Web
Online version of the program for populational genetics.
http://wbiomed.curtin.edu.au/genepop/
Reviews Rating: Not yet Rated Whois Check

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
Reviews Rating: Not yet Rated Whois Check

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
Reviews Rating: Not yet Rated Whois Check

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/
Reviews Rating: Not yet Rated Whois Check

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/
Reviews Rating: Not yet Rated Whois Check

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/
Reviews Rating: Not yet Rated Whois Check

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
Reviews Rating: Not yet Rated Whois Check

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
Reviews Rating: Not yet Rated Whois Check

Sequence Analysis (Bielefeld University Bioinformatics Server)
Collection of sequence analysis tools.
http://bibiserv.techfak.uni-bielefeld.de/intro/seqdept.html
Reviews Rating: Not yet Rated Whois Check

Searching GenBank
Text and similarity searching, provided by the National Center for Biotechnology Information
(NCBI).

http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html
Reviews Rating: Not yet Rated Whois Check

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
Reviews Rating: Not yet Rated Whois Check

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
Reviews Rating: Not yet Rated Whois Check

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/
Reviews Rating: Not yet Rated Whois Check

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/
Reviews Rating: Not yet Rated Whois Check

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/
Reviews Rating: Not yet Rated Whois Check

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
Reviews Rating: Not yet Rated Whois Check

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/
Reviews Rating: Not yet Rated Whois Check

Entrez Browser
Retrieves molecular biology data and bibliographic citations from the NCBI's integrated databases.
http://www.ncbi.nlm.nih.gov/Entrez/
Reviews Rating: Not yet Rated Whois Check

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
Reviews Rating: Not yet Rated Whois Check

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/
Reviews Rating: Not yet Rated Whois Check

 


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