Subject Guides

Neurobiology | Cell & Molecular Biology | General Biology | Ecology & Population Biology | Developmental Biology

Cell and Molecular Biology

General Cell and Molecular Biology

Title: Cell and Molecular Biology Online

URL: www.cellbio.com

Cell and Molecular Biology Online is an informational resource for cell and molecular biologists. Links to online publications, protocols and current research are also included.

Title: Protocol Online

URL: www.protocol-online.org

Protocol-Online provides access to protocols for various subjects such as biochemistry, bioinformatics, genetics and genomics, molecular biology. Also listed are a large amount of protocols for model organisms.

Title: CMS Molecular Biology Resource

URL: http://restools.sdsc.edu

CMS Molecular Biology Resource has a large collection of electronic and Internet tools for a wide variety of subjects. Some of the subjects included are protein analysis, DNA analysis, Biomolecular modeling and Bioinformatics.

Title: Molecular Biology Web Book

URL: www.web-books.com/MoBio/

This E-Book is broken down into chapters based on subjects in Molecular Biology. The chapters are cells and viruses, protein structure and function, various genetics topics, biotechnology and bioinformatics, and diseases. Links to free articles are also available.

Title: Bionformatics.net

URL: http://www.bioinformatics.vg/index.shtml

This directory of bioinformatics and molecular biology provides a series of links and information tools on various subjects, including sequence analysis, molecular biology tools, sequence processing, protein sequence analysis and regulation.

Title: European Bioinformatics Institute

URL: www.ebi.ac.uk/

The European Bioinformatics Institute is in coalition with European Molecular Biology Laboratory.

Their site has a large number of searchable databases of nucleotide sequences, protein sequences and protein structures.

Protein and Enzyme Analysis

Title: Center for Biological Sequence Analysis Databases (CBS)

URL: http://www.cbs.dtu.dk/databases/

The CBS website contains an assortment of information including news, events, research groups, prediction servers, bioinformatics tools, datasets and publications. The prediction servers have information on both nucleotide and amino acid sequences.

Title: ExPASy Proteomics Server

URL: http://kr.expasy.org/

This proteomics server from the Swiss Institute of Bioinformatics includes PROSITE, ENZYME, and GermOnLine, as well as other databases. There are also links to tools and software packages that can be downloaded and used for proteomics and sequencing.

Title: Protein Data Bank

URL: http://www.rcsb.org/pdb/

PDB is home to many 3-D macromolecular protein structures as well as nucleic acid structures. The database is searchable, and can provide information regarding each structure including who discovered it, the source, and the number of polymer chains and atoms.

Title: Cytokines Online Pathfinder Encyclopaedia

URL: http://copewithcytokines.de/

This encyclopaedia for cytokines is browsable and utilizes an alphabetical list. Also provided is structure information, as well as links to journals, symposiums and reviews.

Title: The EF-HandCalcium Binding Protein Data Library

URL: http://structbio.vanderbilt.edu/cabp_database

This online data library is a great source for information on calcium binding proteins. Included about each protein are general information, sequence information, structural information and mutant information.

Title: Protein Kinase Resource

URL: http://pkr.sdsc.edu/html/index.shtml

This source for information on enzymes in the protein kinase family is fully searchable. Searches available include simple search, advanced search, sequence search and proteomics search.

Title: ProtoNet

URL: www.protonet.cs.huji.ac.il

ProtoNet provides an automatic hierarchical classification on a variety of proteins. The database contains over one million protein sequences.

Title: Human Mitochondrial Protein Database

URL: http://bioinfo.nist.gov:8080/examples/servlets/index.html

This website takes information from a variety of databases, including GenBank, LocusLink and PDB to provide ample data on mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function. It also includes information about mitochondrial diseases and links.

Title: Human Protein Reference Database

URL: http://www.hprd.org

The HPR database houses information about human proteins on various levels including domain architecture, post-translational modifications, interactions, and diseases. The database is searchable and browsable and includes illustrations for each protein or enzyme.

Title: Phosphosite

URL: http://www.phosphosite.org

Phosphosite provides information about in vivo phosphorylation sites in both humans and mice. It allows users to view specific phosphorylation sites based on a specific protein sequence.

Title: Sequence Motif Search

URL: http://motif.genome.jp/

Sequence Motif search will search through motif libraries online to see if the protein or nucleic acid sequence entered contains any motifs and identifies them.

Title: Database of Interacting Proteins

URL: http://dip.doe-mbi.ucla.edu/

The Database of Interacting Proteins catalogs experimentally determined interactions between proteins from a variety of sources. All the information is reviewed and inputted by curators. Along with searching functions the website also provides news, statistics, satellite programs, articles and links.

Title: Protein Scanning

URL: http://scansite.mit.edu

SCANSITE has three databases that can be utilized with protein sequence information: motif scan, database search, and sequence search. Some features listed are the ability to scan multiple proteins at once, the ability to search using multiple motifs, and the ability to search databases for two sequence patterns.

Title: ENTREZ Protein

URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein

ENTREZ protein allows entering of a protein or enzyme name to retrieve information, including definition, source, organism, and any significant features of the protein.

Title: ENTREZ Structure

URL: www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=structure

ENTREZ structure allows entering of keyword, protein sequence or nucleotide sequence to retrieve the accurate protein structure. The structures are shown in 3D.

Title: Protein Secondary Structure

URL: http://www.cbi.pku.edu.cn/mirror/GenomeWeb/prot-2-struct.html

This site is a portion of GenomeWeb, and provides a collection of protein secondary structure analysis and information links. For each information link, a summary has been made that provides information on how to use the database and what results to expect.

Title: Predict Protein Server

URL: http://cubic.bioc.columbia.edu/predictprotein/

The Predict Protein Server not only provides resources for structure prediction, but also sequence analysis. It offers many databases to search including multiple sequence alignments, functional motifs, composition-bias, protein domains and fold recognition. It also supplies predictions of various protein structures, such as secondary structure, solvent accessibility, transmemberane helix, globularity, coiled-coil regions, cysteine bonds and structural switching regions.

Genome Analysis (General)

Title: The Human Genome Project

URL: http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml

The HGP site has the most current information about the HGP, including research and education, also included is the history of the project, as well as publications pertaining to the HGP.

Title: American Society of Human Genetics

URL: http://www.ashg.org

The official website of the ASHG provides insight to the world of Human Genetics. There is extensive information about annual meetings, publications, educational resources, projects and policies.

Title: ENTREZ Genome

URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome

Entire genomes of over 1000 viruses and over 100 microbes can be found in Entrez Genome. Both completely sequenced organisms and those for which sequencing is in progress are included. Sequences for viruses and organelles are provided.

Title: Genetics Virtual Library

URL: http://www.ornl.gov/sci/techresources/Human_Genome/genetics.shtml

This Genetics Virtual Library has information on a variety of topics including organisms, countries, human chromosomes and genetic disorders. Each Topic provides a listing of reputable links on the Internet for that topic. Also made available is a list with the most recent additions to the database.

Title: Genome Browser

URL: http://www.ensembl.org/

This browser has genome information on 13 species, including among the most typical species human, mouse and Zebrafish, as well as less common species like chimp, honeybee and dog. Users can search within each species various parameters such as disease, domain, family, gene, peptide, protein and sequence.

Title: Genome Map Viewer

URL: http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?

The Genome Map Viewer provides an extensive graph and information for all the chromosomes in the human genome. After selecting a specific chromosome, a detailed chromosomal map is produced, labeling genes and describing their functions.

Title: Genomic Sequence Searching (BLAST)

URL: http://www.ncbi.nlm.nih.gov/BLAST/

This NCBI site supplies a large amount of searches that can be performed with sequence information. There are nucleotide databases, protein databases, genome databases, translated protein databases and gene expression databases. There is also the ability to compare various sequences.

Title: Stanford Bioinformatics Resource

URL: http://cmgm.stanford.edu

The Stanford bioinformatics resource provides workshops, consultations, hardware and software access for various computers and systems for use in Biomedical research.

Title: Stanford Genome Technology Center

URL: http://sequence-www.stanford.edu/

The Stanford Genome Technology center provides information on the cost-effectiveness of DNA sequencing, and about the genome of S. Cerevisiae. The site also offers publications and project information.

Title: Stanford Genomic Resources

URL: http://genome-www.stanford.edu/

Stanford Genomics Resources provides links to various systematic analysis projects, resources, laboratories, and departments at Stanford University. Genomic research departments are genetics, biochemistry, biological sciences and developmental biology.

URL: Stanford Genome Evolution Center

URL: http://cegs.stanford.edu/index.jsp

The Stanford Genome Evolution Center uses both zebrafish and sticklebacks as model organisms for gene research. It offers extensive links on genomic data for both organisms, such as markers, sequencing and gene mapping.

Genome Analysis for Specific Organisms

Title: WormBase

URL: www.wormbase.org

WormBase is dedicated to the biology and genome of C.elegans. It makes available a BLAST search, batch genes, batch sequences, markers and genetic maps.

Title: FlyBase

URL: http://flybase.bio.indiana.edu/

Flybase is a database of the Drosophila genome, including gene maps, clones, aberrations and anatomy. Flybase and BDGP are joint projects.

Title: FlyNome - Drosophila Nomenclature

URL: http://www.flynome.com/

Flynome answers all the burning questions about the origins of gene names in Drosophila. The database is searchable and by simply searching by the gene name, you will get the story behind the nomenclature.

Title: EcoGene

URL: http://bmb.med.miami.edu/Ecogene/EcoWeb/

EcoGene is a compilation of information about the genes, proteins, and intergenic regions of the E. coli K-12 genome. Genomic maps, databases and files are downloadable from this site.

Title: E.Coli Genetic Stock Center

URL: http://cgsc.biology.yale.edu/

This E. Coli database has information on genotypes for specific strains of E.Coli in the CGSC database. Also available are gene names, properties, linkage maps, gene product information, and mutation information.

Title: TIGR Microbial Database

URL: http://www.tigr.org/tdb/mdb/mdbcomplete.html

TIGR databases contains genomic information for over 20 microbial species, with extensive publication information for each genome.

Title: Mouse Genome Informatics

URL: http://www.informatics.jax.org

Mouse genome Informatics provides accessible data to laboratory mouse genetics, genomics and biology.

Title: Rat Genome Database

URL: http://rgd.mcw.edu/

The Rat Genome Database offers rat genetic and genomic information with the purpose of using the rat as a genetic model for human disease.

Title: Saccharomyces Genome Database

URL: http://www.yeastgenome.org/

The Yeast Genome site provides a variety of tools, such as BLAST, PatMatch, gene sequencing resources and chromosomal features search, which can be applied to the S.cerevisiae genome.

Title: The S.pombe Genome Project

URL: http://www.sanger.ac.uk/Projects/S_pombe

The S.pombe genome project allows searching of the genome, including all protein coding genes, psuedogenes, transposons, and tRNAs. Also included are sequence searches and cloning resources.

Title: TheZebrafish Information Network

URL: http://zfin.org

The Zebrafish Information Network is a comprehensive database on everything there is to know about Zebrafish, including transgenics, wild-type lines, genes, gene expression, genetics maps and publications.

Plant Cell and Molecular Biology

Title: Plant Genome Sequence Searching

URL: http://www.ncbi.nlm.nih.gov/blast/Genome/PlantBlast.shtml?7

This NCBI site has a BLAST search option that will go against all DNA and protein collections mapped in plant genomes.

Title: International Society for Plant Molecular Biology

URL: http://www.uga.edu/~ispmb/

This official site for the ISPMB provides information about the society, as well as publications and links of interest.

Title: Plants and Crops

URL: http://lincoln.nal.usda.gov/index.php?mode=subject&subject=nal_plants&d_subject=Plants%20and%20Crops

Plants and Crops is a list of web resources for plant genomics and other topics related to agriculturally important plants. The site is maintained by the National Agricultural Library.

Title: Plant Gene Expression Center

URL: http://pgec-genome.ars.usda.gov/

The Plant Gene Expression Center offers information on genome sequencing and information regarding their analysis laboratory.

Title: Plant Gene Register

URL: http://www.tarweed.com/pgr/

This register is an electronic publication for articles describing the isolation and DNA sequencing of plant genes. The site is searchable with full text reports from 1995-2000.

Title: Functional Genomics of Plant Phosphorylation

URL: http://plantsp.sdsc.edu/

The FGPP site allows for searching of databases, including BLAST, protein families, and knockouts as well as protein scanning, and predicting myristoylation sites, all in relation to plant phosphorylation.

Title: The Arabidopsis Information Resource

URL: http://arabidopsis.org/

The Arabidopsis Information Resource offers genomic information, as well as analysis tools, links and downloads all about Arabidopsis. It is also searchable for information on genes, DNA, genetic markers, proteins and polymorphisms.

Title: Maize Genetics and Genomics Database

URL:http://www.maizegdb.org/

The Maize GDB contains an assortment of data centers, including gene products, maps, microarrays, phenotypes and sequences. Each data center is searchable by name and sequence.

Nucleic Acids

Title: Nucleic Acid Database (NDB)

URL: http://ndbserver.rutgers.edu

The NDB’s goal is to provide access to nucleic acid structure. The services include an atlas that provides multiple X-ray and NMR images, areas were data can be deposited and downloaded, and a search function.

Title: DNA Translator

URL:http://www.bioinformatics.vg/bioinformatics_tools/JVT.shtml

This translator for only DNA gives information based on a DNA sequence. Once the sequence is entered and the options are set, the program will translate the data.

Title: RNA Modification Database

URL: http://medlib.med.utah.edu/RNAmods/

The RNA Modification Database is an updated and comprehensive listing of post-transcriptionally modified nucleosides from RNA. It is searchable by various parameters including base type and RNA source.

Title: RNABase

URL: www.rnabase.org

The RNA structure database allows for searching and browsing of entries. The entries are broken into the categories, such as structural, functional or experimental technique and contain a variety of references

Title: rRNA Database – The European Ribosomal RNA Database

URL: www.psb.ugent.be/rRNA/index.html

rRNA database compiles all complete or nearly complete small and large subunit ribosomal RNA sequences using a searchable and browsable interface.

Title: RNase P Database

URL: http://jwbrown.mbio.ncsu.edu/RnaseP/home.html

The RNase P Database is a collection of RNase P sequences, sequence alignments, secondary structures, three-dimensional models, and additional information.

Title: ENTREZ Nucleotide

URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide

ENTREZ nucleotide is a searchable database that uses sequences to retrieve data. That data will supply the definition of the sequence, the organism it came from, and any features within that sequence.

Title: Nucleic Acids Research Journal

URL:http://nar.oupjournals.org/

Published by Oxford Journals Online, Nucleic Acids Research Journal gives access to full text articles from 1996 to the current issue, with abstracts available as far back as 1975, as well as the annual database issue.