Web Resources for Molecular Biologists

Sequence Depository

         NCBI Genbank:      
Submit or retrieve genome, gene, and protein sequences from a vast online database. Mostly biomedically focused, may not have updated plant information.
 
         Gramene:
For comparative genomics across crop and model plants.
 
         Legume Information System:
For  comparative genomics across legumes.
 

Sequence Analysis

         NCBI BLAST:
Use  a query sequence (protein or DNA) to find similar sequences from online databases; align multiple sequences of the same type.
 
         ClustalW:Basic sequence alignment, protein or DNA, can do multiple sequences.
 
         Align:
Basic sequence alignment tool.
 
         Serial Cloner 2.6:  
Downloadable program that provides tools to assist in DNA cloning, sequence analysis and visualization.
 
         ApE:
Simple , free downloadable plasmid editor.
 
         CLC Sequence Viewer:Free downloadable program for storing and comparing sequences. Nice, colorful output.
 
         Benchling:
Online tool for virtual cloning, requires login. Stores sequences, creates vector maps with restriction sites, etc.
 
         Vector NTI:
FREE for NCSU, and contains many tools
 
         Geneious:
A commercial bioinformatics software package that includes tools for sequence and chromatogram analysis and analyses of NextGen sequencing data (from assembling a genome to SNP analysis).
 
         UGENE:
Open source bioinformatics software package with many tools for sequence analysis. Not very user friendly.

 

Restriction Site Analysis

         WatCut
 
         NEB Cutter:
 
         Restriction Mapper:

Primer Design

         Primer 3 Plus
 
         PrimerQuest through IDT SciTools

 

Biomath Calculators

         Promega
Molar conversions, ligation ratios, dilutions, temperature conversions, etc.
 
         GraphPad
Molar conversions, dilutions, statistical tools.
 

Molecular Biology & Biochemistry Tools

         JustBio:
Many tools for working with DNA & proteins: translate DNA to protein, reverse complement DNA, calculate protein molecular weight & pI, etc. Requires free registration.
 
         ExPASy (Expert Protein Analysis System)
Dedicated to the analysis of protein sequences and structures.  Links to many bioinformatics resources.
 
         RCSB PDB: (Protein DataBank)
Depository of protein structures, both X-ray crystallography and NMR.

 

OERs (Open Educational Resources)

         NCBI Bookshelf:
Free textbooks available online.
 
         Open Textbook Library:
Free textbooks available online. Usually for general subjects (Biology, Chemistry, etc.).
 
         OER Commons:
Free online modules/simulations/labs (shorter and more specific than textbooks).
 
         BIT OERs:
Our Biotech department’s student-generated resources on molecular biology topics.
 

 Primary Literature

         NCBI Pubmed:
Catalogues abstracts from virtually all scientific journals, easily searchable. Biomedically focused, may not have all plant journals.
 
         Web of Science:
An online subscription-based scientific citation indexing service that provides a comprehensive citation search.  Good for plant journals. 
Access through NCSU libraries.