Short Frame Length Approximation for IRSA

Abstract Background Pseudogenes are non-functional copies of protein coding genes that typically follow a different molecular evolutionary path as compared to functional genes. The inclusion of pseudogene sequences in DNA barcoding and metabarcoding analysis can lead to misleading results. None of the most widely used bioinformatic pipelines used to process marker gene (metabarcode) high throughput sequencing data specifically accounts for the presence of pseudogenes in protein-coding marker genes. The purpose of this study is to develop a method to screen for nuclear mitochondrial DNA segments (nuMTs) in large COI datasets. We do this by: (1) describing gene and nuMT characteristics from an artificial COI barcode dataset, (2) show the impact of two different pseudogene removal methods on perturbed community datasets with simulated nuMTs, and (3) incorporate a pseudogene filtering step in a bioinformatic pipeline that can be used to process Illumina paired-end COI metabarcode sequences. Open reading frame length and sequence bit scores from hidden Markov model (HMM) profile analysis were used to detect pseudogenes. Results Our simulations showed that it was more difficult to identify nuMTs from shorter amplicon sequences such as those typically used in metabarcoding compared with full length DNA barcodes that are used in the construction of barcode libraries. It was also more difficult to identify nuMTs in datasets where there is a high percentage of nuMTs. Existing bioinformatic pipelines used to process metabarcode sequences already remove some nuMTs, especially in the rare sequence removal step, but the addition of a pseudogene filtering step can remove up to 5% of sequences even when other filtering steps are in place. Conclusions Open reading frame length filtering alone or combined with hidden Markov model profile analysis can be used to effectively screen out apparent pseudogenes from large datasets. There is more to learn from COI nuMTs such as their frequency in DNA barcoding and metabarcoding studies, their taxonomic distribution, and evolution. Thus, we encourage the submission of verified COI nuMTs to public databases to facilitate future studies.

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A variable frame length and rate algorithm based on the spectral kurtosis measure for speaker verification

10.21437/interspeech.2010-729 ◽

2010 ◽

Author(s):

Chi-Sang Jung ◽

Kyu J. Han ◽

Hyunson Seo ◽

Shrikanth S. Narayanan ◽

Hong-Goo Kang

Keyword(s):

Speaker Verification ◽

Spectral Kurtosis ◽

Frame Length

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Evalutation of Turbo Decoder Performance Through Software Reference Model

10.4018/978-1-7998-6988-7.ch011 ◽

2022 ◽

pp. 179-197

Author(s):

Manjunatha K. N. ◽

Raghu N. ◽

Kiran B.

Keyword(s):

Reference Model ◽

Channel Noise ◽

Clock Gating ◽

Matlab Simulink ◽

Turbo Decoder ◽

Data Encoding ◽

Frame Length ◽

Noise Type ◽

Turbo Encoder ◽

Number Of Iterations

Turbo encoder and decoder are two important blocks of long-term evolution (LTE) systems, as they address the data encoding and decoding in a communication system. In recent years, the wireless communication has advanced to suit the user needs. The power optimization can be achieved by proposing early termination of decoding iteration where the number of iterations is made adjustable which stops the decoding as it finishes the process. Clock gating technique is used at the RTL level to avoid the unnecessary clock given to sequential circuits; here clock supplies are a major source of power dissipation. The performance of a system is affected due to the numbers of parameters, including channel noise, type of decoding and encoding techniques, type of interleaver, number of iterations, and frame length on the Matlab Simulink platform. A software reference model for turbo encoder and decoder are modeled using MATLAB Simulink. Performance of the proposed model is estimated and analyzed on various parameters like frame length, number of iterations, and channel noise.

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