A multiplex primer design algorithm for target amplification of continuous genomic regions

Download

10.1186-s12859-017-1716-7.pdf

Date

2017-06-19

Author

OZTURK, Ahmet Rasit
Can, Tolga

Metadata

Show full item record

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Item Usage Stats

119
views

98
downloads

Background: Targeted Next Generation Sequencing (NGS) assays are cost-efficient and reliable alternatives to Sanger sequencing. For sequencing of very large set of genes, the target enrichment approach is suitable. However, for smaller genomic regions, the target amplification method is more efficient than both the target enrichment method and Sanger sequencing. The major difficulty of the target amplification method is the preparation of amplicons, regarding required time, equipment, and labor. Multiplex PCR (MPCR) is a good solution for the mentioned problems.

Subject Keywords

Next Generation sequencing, Target amplification, Multiplex PCR, Primer design

URI

https://hdl.handle.net/11511/35742

Journal

BMC BIOINFORMATICS

DOI

https://doi.org/10.1186/s12859-017-1716-7

Collections

Department of Computer Engineering, Article

Suggestions

OpenMETU
Core

A Multiplex primer design algorithm for target amplification of continuous genomic regions Öztürk, Ahmet Raşit; Can, Tolga; Department of Medical Informatics (2016) Targeted Next Generation Sequencing (NGS) assays are cost-efficient and reliable alternatives to Sanger sequencing. For sequencing of very large set of genes, the target enrichment approach is suitable. However, for smaller genomic regions, the target amplification method is more efficient than both the target enrichment method and Sanger sequencing. The major difficulty of the target amplification method is the preparation of amplicons, regarding required time, equipment, and labor. Multiplex PCR (MPCR) is...
A discriminative method for remote homology detection based on n-peptide compositions with reduced amino acid alphabets OĞUL, Hasan; Mumcuoğlu, Ünal Erkan (2007-01-01) In this study, n-peptide compositions are utilized for protein vectorization over a discriminative remote homology detection framework based on support vector machines (SVMs). The size of amino acid alphabet is gradually reduced for increasing values of n to make the method to conform with the memory resources in conventional workstations. A hash structure is implemented for accelerated search of n-peptides. The method is tested to see its ability to classify proteins into families on a subset of SCOP famil...
A General Framework and Novel Transceiver Architecture Based on Hybrid Beamforming for NOMA in Massive MIMO Channels Bayraktar, Murat; Güvensen, Gökhan Muzaffer (2020-06-01) © 2020 IEEE.In this paper, a generic user-grouping based hybrid beamforming framework for mm-wave massive MIMO systems with code domain non-orthogonal multiple access (NOMA), which is considered as an intra-group process, is proposed. It is shown that message passing algorithm (MPA) for decoding sparse code multiple access (SCMA) can be directly applied in this framework without additional complexity. While classical multi-user shared access (MUSA) receiver is adapted for downlink, a novel receiver architec...
A temporal neural network model for constructing connectionist expert system knowledge bases Alpaslan, Ferda Nur (Elsevier BV, 1996-04-01) This paper introduces a temporal feedforward neural network model that can be applied to a number of neural network application areas, including connectionist expert systems. The neural network model has a multi-layer structure, i.e. the number of layers is not limited. Also, the model has the flexibility of defining output nodes in any layer. This is especially important for connectionist expert system applications.
A Semantic Transformation Methodology for the Secondary Use of Observational Healthcare Data in Postmarketing Safety Studies Pacaci, Anil; Gonul, Suat; Sinaci, A. Anil; Yuksel, Mustafa; Laleci Erturkmen, Gokce B. (Frontiers Media SA, 2018-4-30) Background: Utilization of the available observational healthcare datasets is key to complement and strengthen the postmarketing safety studies. Use of common data models (CDM) is the predominant approach in order to enable large scale systematic analyses on disparate data models and vocabularies. Current CDM transformation practices depend on proprietarily developed Extract-Transform-Load (ETL) procedures, which require knowledge both on the semantics and technical characteristics of the source datasets an...

Citation Formats

A. R. OZTURK and T. Can, “A multiplex primer design algorithm for target amplification of continuous genomic regions,” BMC BIOINFORMATICS, pp. 0–0, 2017, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/35742.