ABSTRACT
The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The REPuter program described herein was designed to serve as a fundamental tool in such studies. Efficient and complete detection of various types of repeats is provided together with an evaluation of significance and interactive visualization. This article circumscribes the wide scope of repeat analysis using applications in five different areas of sequence analysis: checking fragment assemblies, searching for low copy repeats, finding unique sequences, comparing gene structures and mapping of cDNA/EST sequences.
Subject(s)
Algorithms , Repetitive Sequences, Nucleic Acid/genetics , Animals , Chromosome Mapping , DNA, Complementary/genetics , Expressed Sequence Tags , Genome , Humans , Sequence Analysis, DNA/methodsABSTRACT
The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The REPuter family of programs described herein was designed to serve as a fundamental tool in such studies. Efficient and complete detection of various types of repeats is provided together with an evaluation of significance, interactive visualization, and simple interfacing to other analysis programs.
Subject(s)
Algorithms , Genome , Repetitive Sequences, Nucleic Acid , Sequence Analysis, DNA/methods , Software , Animals , HumansABSTRACT
SUMMARY: A software tool was implemented that computes exact repeats and palindromes in entire genomes very efficiently. AVAILABILITY: Via the Bielefeld Bioinformatics Server (http://bibiserv.techfak.uni-bielefeld.de/rep uter/).
Subject(s)
DNA/analysis , Genome , Repetitive Sequences, Nucleic Acid , SoftwareABSTRACT
When a family of genes from closely related organisms is known, there is a certain change to extract the corresponding gene from the genome of another related organism. This can be done by polymerase chain reaction, provided that a pair of suitable primers can be designed. In contrast to primer design for a single, known target sequence, systematic primer design for an unknown target given a group of homologues can by no means be done manually. GeneFisher is a software tool which automates this task, and takes special care to make the impact of the manifold design parameters transparent to the user.
