SAB NewsAnd the winners are...Posted 4/14/2004 This study sought to understand more about oligo uses and applications as well as the factors that influence decisions when purchasing custom-made synthetic oligos from commercial suppliers. We pasked our members, "For what reasons do you, or do you not, utilize an in-house software program to design custom synthetic oligos?” Over 800 people contributed to this study and here's what our $20 gift cheque winners had to say: "Do not use in-house a software program to design custom synthetic oligos because the areas of primer interests are rarely compatible with the program's suggestions. For example, I need at times, (a) non-annealing section [usually 5' end] of the primers (i.e., new restriction sites, etc.) to exceed the length of the annealing section and the software program does not allow/account for such modifications; (b) create new restriction sites that are capable of annealing to site; (c) create point mutations; (d) I need in-frame primer designs for subsequent protein expression (i.e., for regulation purposes, protein expression in the development of vaccines, etc.) and the software program does not allow for in-frame primer design; (e) I may need a specific area-whether in-frame or not-to have the primer anneal to (i.e., subtraction hybridization, blocking a restriction endonuclease site, creating site-specific cohesive ends, etc.) and the software program does not allow for such purposes; and (f) the software program is not designed to enable the design of specific automated sequencing primers." --Richard, Lab Director/Supervisor/Coordinator "Except for siRNA design, I do not use an in-house software program to design oligos. I have been working in the field of molecular biology for over eight years now. As expected of a scientist with such experience, I can manually design oligos for a specific purpose while taking into account the GC content, base redundancy etc. It's not that I am not tech savvy. When I do simple things like this manually, they not only hone my basic skills but also bolster my pride in being a first rate molecular biologist." --Vashisht, Post Doctoral Fellow "When designing a primer for a specific gene or cloning experiment, I always rather use in-house software since it allows me to upload the sequences of interest, to annotate them, to perform in silico cloning and/or PCR etc. Again, in-house software packages allow for one to not only to check for primer appropriate design but also to allow for a better representation of product relevance etc. More over, most of the primers that I design are designed manually so I judge by eye the most relevant region that a primer is to be designed. I am not using High through put primer design in which case the automation of such a process would be better via an online software (such as Isect at signal.salk.edu). Finally when designing primers for a specific target sequence, cloning or RT PCR, I rather use in-house software." --Kristophe, Graduate Student/Research Assistant To read some other answers to this question, please click here . Be sure to check out the Study Snapshot for a complete review of this study. Congratulations again to our winners and thank you to all for your participation. |
|
