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 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