DNA-BAR: distinguisher selection for DNA barcoding
نویسندگان
چکیده
DNA-BAR is a software package for selecting DNA probes (henceforth referred to as distinguishers) that can be used in genomic-based identification of microorganisms. Given the genomic sequences of the microorganisms, DNA-BAR finds a near-minimum number of distinguishers yielding a distinct hybridization pattern for each microorganism. Selected distinguishers satisfy user specified bounds on length, melting temperature and GC content, as well as redundancy and cross-hybridization constraints.
منابع مشابه
Highly Scalable Algorithms for Robust String Barcoding
String barcoding is a recently introduced technique for genomic based identification of microorganisms. In this paper, we describe the engineering of highly scalable algorithms for robust string barcoding. Our methods enable distinguisher selection based on whole genomic sequences of hundreds of microorganisms of up to bacterial size, on a well equipped workstation. Experimental results on both...
متن کاملDNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics.
DNA barcoding aims to provide an efficient method for species-level identifications and, as such, will contribute powerfully to taxonomic and biodiversity research. As the number of DNA barcode sequences accumulates, however, these data will also provide a unique 'horizontal' genomics perspective with broad implications. For example, here we compare the goals and methods of DNA barcoding with t...
متن کاملStrength and Limitations of DNA Barcode under the Multidimensional Species Perspective
DNA barcoding aims at providing an efficient method for specieslevel separation using a partial sequence of the mitochondrial COI gene. The efficiency of the barcode in separating species is based on the amount of genetic distance among samples. While in many taxa the species can be efficiently identified through the barcode, other situations cannot be treated by this approach. The causes for s...
متن کاملAppraisal of the entire mitochondrial genome for DNA barcoding in birds
DNA barcoding based on a standardized region of 648 base pairs of mitochondrial DNAsequences from Cytochrome C Oxidase 1 (COX1) is proposed for animal species identification.Recent studies suggested that DNA barcoding has been effective for identifying 94% of birdspecies. The proposed threshold of 10 times the average intraspecific variation could be used forthe identification and delimitation ...
متن کاملDNA Barcoding: a new tool with wide array of applications
DNA barcoding is a new term introduced in to scientific literatures by Hebert and coworkers almost a decade ago. The concept of barcoding alone is well-known to the public: a series of black bars printed on many commercial products (Universal Product Code), which are used to distinguish different products. Advances made in molecular biology and molecular techniques late 20th century e.g. sequen...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
- Bioinformatics
دوره 21 16 شماره
صفحات -
تاریخ انتشار 2005