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March 2007, SoftGenetics - Sequence Assembly and Mutation Detection with Mutation Surveyor®:

Introduction

Within the past decade, shotgun sequencing has been demonstrated to be a powerful tool in sequencing the genomes of several organisms (1). Dueto limitations of only several hundred consecutive bases with adequate resolution, techniques needed to be developed to piece together billions ofbases into consecutive order. There are several emerging technologies that make sequencing faster and generate short sequences. 454 LifeSciences™ utilizes the pyrosequencing technique and generates sequences that are about 100 bases in length (2), Illumina®’s sequencing-by-synthesismethod yields read lengths of about 25 base pairs (3), and the sequencing-by-ligation technique yields fragments about 20 base pairs in length (4).The genomes from many organisms including Drosophila melanogaster, Escherichia coli, mouse and of course human have been fully sequenced andassembled and are available in multiple databases for use by the public. However, many researchers are not working with sequences that have beenassembled and published.
For the genetic analysts working with sequences that do not have genomic references, Mutation Surveyor is a powerful tool capable of taking a groupof sequences and assembling them into one long reference file. Just as the shotgun sequencing method when used to sequence the human genomerequired these short sequences to be assembled, many other projects require the same functionality. Mutation Surveyor is capable of assemblingsequences of many formats including *ab1, *abi and *scf. The resulting text file containing a single nucleotide text string can then be utilized directlyby the software as the reference file or annotated similarly to a GenBank file for identification of the coding sequence, variations and more.
In addition to its short sequence assembly tool, Mutation Surveyor is a powerful genetic analysis package capable of comparing samples to referencesequences and easily finding nucleotide and amino acid variations. All types of single nucleotide polymorphisms (SNPs) including homozygoussubstitutions, heterozygous substitutions with as little as 5-10% contribution from the minor allele and insertions and deletions (INDELs) can bedetected with the click of only a couple buttons. Mutation Surveyor provides an accuracy >99% in detecting homozygous and heterozygous SNPs (5), when both forward and reverse traces are of Phred 20 quality. In addition, the complex heterozygous INDELs are deconvoluted from each otheryielding two clean traces for easy identification of nucleotide variations.

 

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