Submit or retrieve genome, gene, and protein sequences from a vast online database. Mostly biomedically focused, may not have updated plant information.
For comparative genomics across crop and model plants.
Legume Information System:
For comparative genomics across legumes.
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.
Basic sequence alignment tool.
Serial Cloner 2.6:
Downloadable program that provides tools to assist in DNA cloning, sequence analysis and visualization.
Simple , free downloadable plasmid editor.
CLC Sequence Viewer:Free downloadable program for storing and comparing sequences. Nice, colorful output.
Online tool for virtual cloning, requires login. Stores sequences, creates vector maps with restriction sites, etc.
FREE for NCSU, and contains many tools
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).
Open source bioinformatics software package with many tools for sequence analysis. Not very user friendly.
Restriction Site Analysis
Primer 3 Plus
PrimerQuest through IDT SciTools
Molar conversions, ligation ratios, dilutions, temperature conversions, etc.
Molar conversions, dilutions, statistical tools.
Molecular Biology & Biochemistry Tools
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)
Free textbooks available online.
Open Textbook Library:
Free textbooks available online. Usually for general subjects (Biology, Chemistry, etc.).
Free online modules/simulations/labs (shorter and more specific than textbooks).
Our Biotech department’s student-generated resources on molecular biology topics.
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.