Mutation Surveyor

GeneMarker is multi-function DNA genotyping software, having the following functions: DNA polymorphism analysis based on microsatellite DNA (or STR), high-throughput SNP analysis, AFLP analysis. GeneMarker has special characters of high sensitivity, stable performance and simple operation.
 

1.The related biology background knowledge

 
a.Microsatellite DNA (STR)
Human genomic DNA has 3 billion base pairs, and 10 percent of them are short repeat sequences, named microsatellite DNA. Microsatellite (MS) refers to the simple repeated sequences shorter than 10 nucleic acids, also called short tandem repeat (STR). Microsatellite is a kind of repeat sequence in all over the human genome. They usually are 2 to 6 bp repeats, such as (CA)n, (GT)n, (CAG)n and so on. Among them, (CA)n is the most frequent sequence. Their length is determined by the copies of repeat unit. Microsatellite is a kind of highly polymorphic genetic marker, which is not only used in the construction of genomic linkage map, gene location and cloning, but also in the linkage analysis and gene diagnosis of genetic disease. They can be inherited stably and is a very good genetic marker.
b.Amplified Fragment Length Polymorphism (Amp-FLP)
AFLP (Amplified Fragment Length Polymorphism) technique is the most novel method in constructing DNA fingerprinting in the world now. It has many advantages which are abundant band, high sensitivity, good stability, speed and high efficiency. Because during AFLP lots of fragments will be produced in one specific kind of species and seldom in another, it is safe to say AFLP is a new and powerful DNA fingerprinting technique.
 
The application foreground of AFLP:
1. To construct genetic linkage map
2. To quickly identify the molecular markers highly linked with the destination genes.
3. To study gene expression and regulation.
4. To study evolution and biology classification.
5. To do DNA methylation study.
 

2.The innovation and technique characters of GeneMarker

 
Innovations:
a) Adopting Smich Waterson algorithm, efficiently enhancing the accuracy of Size-call changing
b) Innovative Size Scoring system: Using unique score to indicate Size-Call quality of sample, in order to help users checking the results of Size-Call. Based on the system, GeneMarker can automatically judge the function of Size-Standard.
c) Original peak scoring system: according to the signal quality and its distributing rule, each allele peak can be scored.
d) Original panel template automatic construction: adopting Max/Average method, automatic generate all kinds of panel templates from sample data. This function efficiently user’s work of constructing new templates. This method is also including optimized intellectual grouping algorithm.
e) Optimized Gel image recovery: adopting optimized mixing color algorithm to realize the recovery and color mixing from different channels.
 
Technique characters:
a) User-friendly operation and interface, simple to use, highly intellectual characters.
b) High speed, stable running can meet the needs of high-throughput computation
c) High performance of accuracy and sensitivity comparing with other related software.
d) Supporting many sorts of data including ABI, MegaBase, and so on
e) Supporting Windows 98/NT/2000/XP/2003 several operating systems.
f) Besides to provide powerful final version to formal users, we also provide free or low-price and simple-function share version to some research institutions or university.
 

3.Function

 
a) Linkage analysis and genetic map construction
b) LOH analysis in cancer research field
c) The genomic location analysis of related genes of complex diseases ( for example, cancer)
d) Polymorphism research in evolution field
e) Paleontology related study
f) High-throughput analysis of SNP, based on single nucleic acid elongation method.
 

4.The application fields

 
a) Supporting many sorts of source data including ABI, FSA, SCF, ESD (MegaBase), and so on.
b) Size-Call: precise changing for original data according to size standard
c) Allele-Call: obtaining genotyping results according to panel templates
d) Forensic analysis: according ladder information, further precisely aligning the samples
e) Output report: supporting allele list, allele count, fragment, AFLP formats, and horizontal or vertical styles
f) Printing report: user can custom the reporting contents and preview the printing results.
g) Size calibration: manually emendation of the size-call results
h) Scoring system: based on statistics, generating size-call and allele peak quality score, guiding users to edit the results.
i) Edit and manage the Panel/Size templates, helping users to build new templates.
j) Supporting projection file: this can manage and save batch of data and compute results.