New softwares for automated microsatellite marker development.
Microsatellites are repeated small sequence motifs that are highly polymorphic and abundant in the genomes of eukaryotes. Often they are the molecular markers of choice. To aid the development of microsatellite markers we have developed a module that integrates a program for the detection of microsatellites (TROLL), with the sequence assembly and analysis software, the Staden Package. The module has easily adjustable parameters for microsatellite lengths and base pair quality control. Starting with large datasets of unassembled sequence data in the form of chromatograms and/or text data, it enables the creation of a compact database consisting of the processed and assembled microsatellite containing sequences. For the final phase of primer design, we developed a program that accepts the multi-sequence 'experiment file' format as input and produces a list of primer pairs for amplification of microsatellite markers. The program can take into account the quality values of consensus bases, improving success rate of primer pairs in PCR. The software is freely available and simple to install in both Windows and Unix-based operating systems. Here we demonstrate the software by developing primer pairs for 427 new candidate markers for peanut.
Department of Computer Science, Catholic University of Goiás, Brazil.
Wellington
W
Martins
Daniel
D
de Sousa
Karina
K
Proite
Patrícia
P
Guimarães
Marcio
M
Moretzsohn
David
D
Bertioli
D010367:Arachis / Q000235:genetics; D017931:DNA Primers; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D005819:Genetic Markers; D015698:Genomic Library; D020407:Internet; D018895:Microsatellite Repeats; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D012984:Software
D017931:DNA Primers; D005819:Genetic Markers