Overview

Sequence Quickie-Calc from Molecular Programming LLC was designed as a highly simplified aid to performing the routine computations of molecular biology. It can perform simple DNA manipulations, calculate length and base content, and make Tm estimations for oligonucleotides. It also makes mole-to-mass and mass-to-mole calculations. Protein-analysis features include hydropathy and hydrophilicity plots, plus length, amino-acid-content, isoelectric-point, and molecular-weight calculations. These functions are presented in an onscreen format reminiscent of a calculator with the different functions driven by "buttons."

How Long Did It Take to Learn to Use It Productively?

A few minutes.

Product Quality

Customizability

None.

Ability to Program in Scripts, Add Extension Modules, etc.

None.

Ability to Import and Export in Different File Formats

Imports ASCII text files. It has no export options, although a sequence can be copied to the clipboard for insertion into a word-processing program.

Useful or Unusual Features

Possibly the most attractive feature of this program is the onscreen interface. Nearly all of the sequence manipulations are achieved in just a couple of mouse clicks. The program can easily sit on your computer desktop and be kept handy for minor calculations.

Limitations

Regrettably, while the concept is interesting, technology has bypassed this program. Most of the manipulations and calculations this program performs can be executed using software freely available via the Internet, and those programs, almost without exception, do a much better job. I was surprised to discover that this program searches for only one restriction site at a time and, once it is found, merely highlights the relevant sequence. Indeed, this function is best considered as a motif search and can be used as such. Expanding on a search for a specific restriction site would be difficult to carry out. Generating a restriction map for a sequence under analysis would require a pencil, ruler, and drawing pad. While it is possible to update the list of restriction sites from the developer's Web site, it is impossible to add manually a new recognition site to the list. Other useful functions such as identifying subsets of restriction sites, e.g., single or double cutters and non-cutters, are well beyond the capacity of this software. Manipulating sequence is potentially risky in that it is possible to invert your sequence, complement it, or derive the reverse complement, but this happens without a trace. Once again you need paper and pencil to remind yourself of the operations that have been performed.

When using the larger sequence analysis programs for analysis, I am often vexed by the generation of new files every time a manipulation is performed. However, I am also uncomfortable with Sequence Quickie-Calc's lack of signposts. This lack might easily be resolved by changing font color with each manipulation. Translating the DNA sequence to protein is likely to cause trouble. First, there is no means of searching for open reading frames. Then there is no means of selecting a frame to translate; should you be so fortunate as to stumble across the desired polypeptide, you cannot highlight it and perform the various protein analyses available to you.

I suspect that this program is best used to perform analyses of short sequences. Possibly those whose research requires repetitive sequencing of short fragments might find this a very rapid way to screen large piles of relatively similar data.

Comparisons with Similar Software

This program cannot be compared with programs such as Vector NTI, Lasergene, or Omiga, all of which are much more expensive. However, it cannot easily compete with programs available free online such as WebCutter 2.0. If buying the more expensive sequence analysis programs is not an option, spending the money on an Internet connection to give you access to sites such as the CMS Molecular Biology Resource might be a better use of limited funds.

Technical Support and Documentation

Documentation is adequate. There is online help, but no more than can be obtained by flipping through the provided manual. This isn't a very demanding program, and you are unlikely to require telephone or offline help.

Target Users

As mentioned above, possibly someone who needs a means of rapidly checking raw sequence data might find this program handy. Others who might find it useful are high-school teachers and students, who could use it as a tool to assist in the teaching of molecular biology. Quickie-Calc might be a useful tool for introducing students to the way DNA and protein sequences can be analyzed and manipulated. People working in biotechnology fields involving custom-synthesis procedures might also find Quickie-Calc useful for checking or screening short DNA or peptide sequences and making rapid calculations.