KnowledgeBase

Useful DNA Sequence Analysis Links

Nucleic Acids Research Annual Web Server Issue

The 2010 Web Server Issue of Nucleic Acids Research is the eighth in a series of annual special issues dedicated to web-based software resources for analysis and visualization of molecular biology data. It is freely available online under NAR’s open access policy. The present issue reports on 122 web servers.

NCBI

• NCBI Entrez - the 8th wonder of the world
• links for "Cycle Sequencing" from the NCBI Bookshelf
• NCBI Blast offers bl2seq alignment of two fasta sequences and COBALT (constraint-based multiple alignment tool) for multiple sequence (protein) alignment.
  

Other Sequencing Tools and Discussion

• Tools for sequence analysis - another awesome resource from EMBL-EBI
  
• Notes on Template purification Some practical hints regarding preparation of templates for automated fluorescent cycle sequencing.
• Direct Sequencing of PCR Products Primer Robert Lyons at the U of Michigan has written a very nice intro to this occassionally frustrating technique.
• PCR Rescue: Making one band from many The bitesizebio.com PCR-Rescue method for gel separation of multiple products, capture the fragment of interest, and reamplify
  
• Open source Sequence Aligment Tools Handy list of on-line tools (some of the links are old)
• Exo-SAP IT PCR Cleanup Kit manual An innovative method for 'cleaning up' PCR products for direct sequencing.
  
• 10-tips-for-better-DNA-gel-extraction Bitesize Bio post on improving DNA extraction from agarose gels
• GeoSpiza's FinchTalk blog Nice discussion of automated sequencer errors and their impact on sequence assembly.

Useful Oligo Synthesis Links

• Glen Research Additional links from Glen Research - our source for high quality reagents
• LNA monomers Probes synthesized with linked nucleic acid (LNA) monomers have higher melting temperatures for improved discrimination of exact vs mismatched sequences.
• Table of extinction coeficients Data for standard bases, base analogs and labels
• Primer3 A highly customizable primer designer from MIT
• BatchPrimer3 Uses primer3 as the design engine and can generate a batch of primers of different sorts
  
• NCBI's Gateway Website for RNA Interference Excellent primer for silencing genes with RNAi
• Essential formulae for oligonucleotides
• NCBI's RNAi Probes Resource Technical information for RNA interference experiments
• GMP synthesis and PAGE purified oligonucleotides Oligos Etc can do PAGE purification and GMP synthesis for clinical (and pre-clinical) applications.
• Oligo Calc An oligonucleotide properties calculator. Very nice for Tm, molecular weight, mass to concentration calculations.
  

Molecular Biology References

Enzymes used in molecular biology: a useful guide. By Laure Ritteé and Bernard Perbal.

Wiley Current Protocols OHSU LIbrary subscription

Addgene is a global, non-profit plasmid repository dedicated to making it easier for scientists to share. Here is a guide to Addgene's empty vector backbones.