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Department of microbiology and molecular genetics

Bioinformatics and Molecular Biology Resources

General sites

National Center for Biotechnology Information
This site contains links to PubMed (Medline), ENTREZ (protein and nucleotide databases), and BLAST (alignment tool).

Molecular Biology Gateway
Contains links to many molecular resources on the web, including Molecular Biology protocols, and PCR techniques.

The Institute for Genomic Research (TIGR) Database
Contains access to completely sequence genomes of Bacteria, as well as Archea. Currently sequencing projects include both prokaryotic and eukaryotic genomes.

ExPASy
Molecular server that is dedicated to the analysis of protein and nucleic acid sequences.

Molecular Biology Resources at University of Lincoln-Nebraska
Another site that contains links to Internet-accessible tools and resources.

The Sequence and Structure Searching Site
Run out of Stanford, this site lists sites dedicated to the aid of biomolecular sequence and structure searching.

European Bioinformatics Institute (EBI)
European Bioinformatics Institute (EBI) is a centre for research and services in bioinformatics. The Institute manages databases of biological data including nucleic acid, protein sequences and macromolecular structures.

Gene Databases Links
Links to various gene and genome sequence databases.

Vector Database
List various vectors and their descriptions for different organisms

Genome Sequencing Sites

Genome Sequencing Center
Listings of various genome sequencing projects including the Human genome.

National Center for Genome Resources
Information and links to various genome related projects.

DOE Microbial genome Program Projects
List of completed and ongoing genome sequencing projects.

The Sanger Centre
The studies in this research group are aimed at developing computational approaches for analysis of nucleotide and protein sequences and structures as well as understanding structural and functional organization of genetic signals encoded in genome sequences.

GenomeNet
GenomeNet is a Japanese network of database and computational services for genome research and related research areas in molecular and cellular biology. GenomeNet was established in September 1991 under the Human Genome Program (HGP) of the Ministry of Education, Science, Sports and Culture (MESSC).

DNA Sequence Analysis

Sequence manipulation tools:

Reverse complement
Sequence ORIENTATION conversion. One can reverse, complement, or reverse and complement a DNA sequence.

Translate tool
Translation of DNA nucleotide sequence to a protein sequence.

Primer Design, PCR, Restriction mapping:

Tm Determination
Can determine oligonucleotide melting temperature.

Primer design:

Primers!
Design your own primer on the Internet and download free PCR software.
Primer Design
Java applet that allows you to design your own primers, and control all the variables.

Codon Usage Database
A query box to search a codon usage table for an organism, is presented. Search can be done with Latin name or its sub-string of organism. Useful for cration of primers and probes.

Structure and Function:

Prediction of promoter regions:

Proscan
Program for identifying eukaryotic promoters.

General Gene Recognition Programs
A set of programs for eukaryotic promoter predictions and gene identification.

Protein coding region prediction in:

FramePlot
Bacterial DNA.

Gene Finder
Eukaryotic DNA

ORF Finder
Bacterial and Eukaryotic DNA

GeneMark
Email based protein encoding regions from both prokaryotic and eukaryotic species.

Genie Interactive
Genie is a gene identification tool originally developed at the University of California, Santa Cruz. The program uses a Hidden Markov Model (HMM) as a high-level grammar representing gene structure.

Glimmer
Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria and archaea. Glimmer (Gene Locator and Interpolated Markov Modeler) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA.

Sequences retrieval from databases:

ENTREZ (nucleotide database)
To find a known DNA sequence by gene or protein name, accession number, publication, author, etc.

Search for homologues, sequence comparison:

BLAST
Use to search for sequence homology between your sequence and those in the databases. BLASTN will perform search in DNA sequences; BLASTX will translate your sequence in all 6 frames and perform a search in protein sequences.

Fasta 3
Sequence similarity and homology searching against nucleotide and protein database using Fasta3.

Protein Sequence Analysis

Sequences retrieval from databases:

ENTREZ (protein database)
Use to find a known protein sequence by gene (protein) name, accession number, publication, author, etc.

SWISS-PROT
Annotated protein database maintained by the University of Geneva. SWIIS-PROT prides itself on having the most comprehensive annotation available.

DBGET/LinkDB
DBGET is a simple database retrieval system for finding and obtaining specific entries of diverse databases. Here a database is simply considered a sequential collection of entries, which may be stored in a single file or multiple files. Because each entry of a database is given a unique identifier, molecular biology databases in the world can be retrieved uniformly by the combination of the database name and the identifier.

Sequence Retrieval System
Can be used to retrieve sequences from a variety of different databases in a simplified and easy to use format.

Search for homologues, sequence comparison:

BLAST
BLAST 2.0 will displays the results in a graphical view and take care of gaps in your sequences. Don't forget to choose "blastp" option, since you're doing protein search!

PSI-BLAST
Position-Specific Iterated BLAST is a derivative of BLAST that performs iterative database searches and can uncover many protein relationships that are not detectable via one-pass database searches.

BLAST 2 Sequences
This tool provides the alignment of any two sequences using the BLAST engine for local alignment.

Multiple sequence alignment

ClustalW
Use this program to align multiple sequences of DNA/Protein. Choose "Multiple sequence alignment" option on this server, and follow instructions. It is helpful to have all the sequences that you want to align in FASTA format in a Word file. Simply cut them from there and paste into the window of your ClustalW alignment page.

ClustalW in color
Choose "Yes" option in the "Color" window and don't change any other default.

Clustal X
Clustal X is a downloadable program that can generate multiple alignments of protein and DNA sequences. It can also generate phylogenetic trees based on the alignments.

Consensus
Using a custom Peral Script, a consensus can be generated from a multiple alignment in either Clustal or MSF format.

Blocks, structural elements, and domains:

Blocks
Can identify conserved blocks in multiple alignments.

MPEx
Can identify transmembrane regions in membrane protein sequences.

ProDom
Can identify known functional domains in your sequences.

Secondary structure predictions:

PHD
PredictProtein (part of the Predict Protein server), the most popular server for predicting the secondary structure of a protein sequence.

PREDATOR (submitting form)
Another useful program for predicting secondary structure. You can also visit the Predator home page for more information.

PROTSCALE
In addition to predicting secondary structure, it also predicts a variety of protein functions.

Protein Structure - 3D:

Protein Database
An archive of experimentally determined three-dimensional structures of biological macromolecules.

Swiss-Model Protein
SWISS-MODEL is an Automated Protein Modeling Server in Geneva, Switzerland.

Phylogenetic Analysis

Programs:

PHYLIP
One of the best free, downloadable programs available on the Internet that can be used to analyze the phylogenetic relationship between different sequences.

GeneDoc Program
Phylogenetic program that is available for download.

TreeView
Tree drawing program for Windows and Macintosh. Can be used to view PHYLIP generated phylogeny trees.

Treecon
A retail phylogenetic tree construction program for Windows. You can download a free trial version.

Darwin
Data Analysis and Retrieval With Indexed Nucleotide/peptide sequences. Can send out your sequence for analysis. It will be emailed back to you in postscript format, which you can then print.

Phylogeny Software Lists:

Phylogeny Software List
A complete list of phylogeny software. Contains descriptions of both free and retail software available.

Phylogeny Laboratory
Another list of a phylogeny software packages available.

Downloadable Programs and Plug-ins

Downloadable Programs:

RasMol
Free software for looking at PDB files. PDB files are 3D structures of DNA/proteins.

Swiss-PDB Viewer
A free viewer that can analyze multiple proteins at the same time. Can be used to compare fold similarities and analyze structural alignments.

Pov-Ray
When used with Swiss-PDB viewer the rendered output image appears much sharper and the colors are more vivid.

Cn3D Viewer
Easy-to-use interactive viewer for molecular structures retrieved from Entrez. You can visit the Cn3D home page for more information.

Plug-ins:

Chime 3D Homepage
Plug-in for both Netscape and Internet Explorer. It allows for the viewing of 3D files (PDB, etc.) inside a webpage.

On-Line Journals

American Society of Microbiology Journals (Homepage)

Includes:

Elsevier Trends Journals (Homepage)

Includes

Other On-line Journals

If you have any comments of suggestions regarding the resource page; or if you have a link that you wish to add to the list, please contact Dr. Igor Zhulin.

School of Medicine - Graduate School - Loma Linda University

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