Identification of protein coding regions using the modified Gabor-wavelet transform

An important topic in genomic sequence analysis is the identification of protein coding regions. In this context, several coding DNA model-independent methods based on the occurrence of specific patterns of nucleotides at coding regions have been proposed. Nonetheless, these methods have not been completely suitable due to their dependence on an empirically predefined window length required for a local analysis of a DNA region. We introduce a method based on a modified Gabor-wavelet transform (MGWT) for the identification of protein coding regions. This novel transform is tuned to analyze periodic signal components and presents the advantage of being independent of the window length. We compared the performance of the MGWT with other methods by using eukaryote data sets. The results show that MGWT outperforms all assessed model-independent methods with respect to identification accuracy. These results indicate that the source of at least part of the identification errors produced by the previous methods is the fixed working scale. The new method not only avoids this source of errors but also makes a tool available for detailed exploration of the nucleotide occurrence.

A flexible side information generation framework for distributed video coding

One of the most efficient approaches to generate the side information (SI) in distributed video codecs is through motion compensated frame interpolation where the current frame is estimated based on past and future reference frames. However, this approach leads to significant spatial and temporal variations in the correlation noise between the source at the encoder and the SI at the decoder. In such scenario, it would be useful to design an architecture where the SI can be more robustly generated at the block level, avoiding the creation of SI frame regions with lower correlation, largely responsible for some coding efficiency losses. In this paper, a flexible framework to generate SI at the block level in two modes is presented: while the first mode corresponds to a motion compensated interpolation (MCI) technique, the second mode corresponds to a motion compensated quality enhancement (MCQE) technique where a low quality Intra block sent by the encoder is used to generate the SI by doing motion estimation with the help of the reference frames. The novel MCQE mode can be overall advantageous from the rate-distortion point of view, even if some rate has to be invested in the low quality Intra coding blocks, for blocks where the MCI produces SI with lower correlation. The overall solution is evaluated in terms of RD performance with improvements up to 2 dB, especially for high motion video sequences and long Group of Pictures (GOP) sizes.

Adaptive deblocking filter for transform domain Wyner-Ziv video coding

Wyner-Ziv (WZ) video coding is a particular case of distributed video coding, the recent video coding paradigm based on the Slepian-Wolf and Wyner-Ziv theorems that exploits the source correlation at the decoder and not at the encoder as in predictive video coding. Although many improvements have been done over the last years, the performance of the state-of-the-art WZ video codecs still did not reach the performance of state-of-the-art predictive video codecs, especially for high and complex motion video content. This is also true in terms of subjective image quality mainly because of a considerable amount of blocking artefacts present in the decoded WZ video frames. This paper proposes an adaptive deblocking filter to improve both the subjective and objective qualities of the WZ frames in a transform domain WZ video codec. The proposed filter is an adaptation of the advanced deblocking filter defined in the H.264/AVC (advanced video coding) standard to a WZ video codec. The results obtained confirm the subjective quality improvement and objective quality gains that can go up to 0.63 dB in the overall for sequences with high motion content when large group of pictures are used.

Statistical motion learning for improved transform domain Wyner-Ziv video coding

Wyner - Ziv (WZ) video coding is a particular case of distributed video coding (DVC), the recent video coding paradigm based on the Slepian - Wolf and Wyner - Ziv theorems which exploits the source temporal correlation at the decoder and not at the encoder as in predictive video coding. Although some progress has been made in the last years, WZ video coding is still far from the compression performance of predictive video coding, especially for high and complex motion contents. The WZ video codec adopted in this study is based on a transform domain WZ video coding architecture with feedback channel-driven rate control, whose modules have been improved with some recent coding tools. This study proposes a novel motion learning approach to successively improve the rate-distortion (RD) performance of the WZ video codec as the decoding proceeds, making use of the already decoded transform bands to improve the decoding process for the remaining transform bands. The results obtained reveal gains up to 2.3 dB in the RD curves against the performance for the same codec without the proposed motion learning approach for high motion sequences and long group of pictures (GOP) sizes.

Design and performance of a novel low-density parity-check code for distributed video coding

Low-density parity-check (LDPC) codes are nowadays one of the hottest topics in coding theory, notably due to their advantages in terms of bit error rate performance and low complexity. In order to exploit the potential of the Wyner-Ziv coding paradigm, practical distributed video coding (DVC) schemes should use powerful error correcting codes with near-capacity performance. In this paper, new ways to design LDPC codes for the DVC paradigm are proposed and studied. The new LDPC solutions rely on merging parity-check nodes, which corresponds to reduce the number of rows in the parity-check matrix. This allows to change gracefully the compression ratio of the source (DCT coefficient bitplane) according to the correlation between the original and the side information. The proposed LDPC codes reach a good performance for a wide range of source correlations and achieve a better RD performance when compared to the popular turbo codes.

BlastR--fast and accurate database searches for non-coding RNAs.

We present and validate BlastR, a method for efficiently and accurately searching non-coding RNAs. Our approach relies on the comparison of di-nucleotides using BlosumR, a new log-odd substitution matrix. In order to use BlosumR for comparison, we recoded RNA sequences into protein-like sequences. We then showed that BlosumR can be used along with the BlastP algorithm in order to search non-coding RNA sequences. Using Rfam as a gold standard, we benchmarked this approach and show BlastR to be more sensitive than BlastN. We also show that BlastR is both faster and more sensitive than BlastP used with a single nucleotide log-odd substitution matrix. BlastR, when used in combination with WU-BlastP, is about 5% more accurate than WU-BlastN and about 50 times slower. The approach shown here is equally effective when combined with the NCBI-Blast package. The software is an open source freeware available from www.tcoffee.org/blastr.html.

Cellular source and mechanisms of high transcriptome complexity in the Mammalian testis.

Understanding the extent of genomic transcription and its functional relevance is a central goal in genomics research. However, detailed genome-wide investigations of transcriptome complexity in major mammalian organs have been scarce. Here, using extensive RNA-seq data, we show that transcription of the genome is substantially more widespread in the testis than in other organs across representative mammals. Furthermore, we reveal that meiotic spermatocytes and especially postmeiotic round spermatids have remarkably diverse transcriptomes, which explains the high transcriptome complexity of the testis as a whole. The widespread transcriptional activity in spermatocytes and spermatids encompasses protein-coding and long noncoding RNA genes but also poorly conserves intergenic sequences, suggesting that it may not be of immediate functional relevance. Rather, our analyses of genome-wide epigenetic data suggest that this prevalent transcription, which most likely promoted the birth of new genes during evolution, is facilitated by an overall permissive chromatin in these germ cells that results from extensive chromatin remodeling.

Hybrid turbo FEC/ARQ systems and distributed space-time coding for cooperative transmission

Cooperative transmission can be seen as a "virtual" MIMO system, where themultiple transmit antennas are in fact implemented distributed by the antennas both at the source and the relay terminal. Depending on the system design, diversity/multiplexing gainsare achievable. This design involves the definition of the type of retransmission (incrementalredundancy, repetition coding), the design of the distributed space-time codes, the errorcorrecting scheme, the operation of the relay (decode&forward or amplify&forward) and thenumber of antennas at each terminal. Proposed schemes are evaluated in different conditionsin combination with forward error correcting codes (FEC), both for linear and near-optimum(sphere decoder) receivers, for its possible implementation in downlink high speed packetservices of cellular networks. Results show the benefits of coded cooperation over directtransmission in terms of increased throughput. It is shown that multiplexing gains areobserved even if the mobile station features a single antenna, provided that cell wide reuse of the relay radio resource is possible.

Source separation techniques applied to linear prediction

The prediction filters are well known models for signal estimation, in communications, control and many others areas. The classical method for deriving linear prediction coding (LPC) filters is often based on the minimization of a mean square error (MSE). Consequently, second order statistics are only required, but the estimation is only optimal if the residue is independent and identically distributed (iid) Gaussian. In this paper, we derive the ML estimate of the prediction filter. Relationships with robust estimation of auto-regressive (AR) processes, with blind deconvolution and with source separation based on mutual information minimization are then detailed. The algorithm, based on the minimization of a high-order statistics criterion, uses on-line estimation of the residue statistics. Experimental results emphasize on the interest of this approach.

Interference cancellation in two-path successive relay system with network coding

This paper proposes a novel interference cancellation algorithm for the two-path successive relay system using network coding. The two-path successive relay scheme was proposed recently to achieve full date rate transmission with half-duplex relays. Due to the simultaneous data transmission at the relay and source nodes, the two-path relay suffers from the so-called inter-relay interference (IRI) which may significantly degrade the system performance. In this paper, we propose to use the network coding to remove the IRI such that the interference is first encoded with the network coding at the relay nodes and later removed at the destination. The network coding has low complexity and can well suppress the IRI. Numerical simulations show that the proposed algorithm has better performance than existing approaches.

Sequence characterization of coding regions of the myostatin gene (GDF8) from Brazilian Murrah buffaloes (Bubalus bubalis) and comparison with the Bos taurus sequence

Within about 30 years the Brazilian buffalo (Bubalus bubalis) herd will reach approximately 50 million head as a result of the great adaptive capacity of these animals to tropical climates, together with the good productive and reproductive potential which make these animals an important animal protein source for poor and developing countries. The myostatin gene (GDF8) is important in the physiology of stock animals because its product produces a direct effect on muscle development and consequently also on meat production. The myostatin sequence is known in several mammalian species and shows a high degree of amino acid sequence conservation, although the presence of non-silent and silent changes in the coding sequences and several alterations in the introns and untranslated regions have been identified. The objective of our work was to characterize the myostatin coding regions of B. bubalis (Murrah breed) and to compare them with the Bos taurus regions looking for variations in nucleotide and protein sequences. In this way, we were able to identify 12 variations at DNA level and five alterations on the presumed myostatin protein sequence as compared to non double-muscled bovine sequences.

Sequence characterization of coding regions of the myostatin gene (GDF8) from Brazilian Murrah buffaloes (Bubalus bubalis) and comparison with the Bos taurus sequence

Within about 30 years the Brazilian buffalo (Bubalus bubalis) herd will reach approximately 50 million head as a result of the great adaptive capacity of these animals to tropical climates, together with the good productive and reproductive potential which make these animals an important animal protein source for poor and developing countries. The myostatin gene (GDF8) is important in the physiology of stock animals because its product produces a direct effect on muscle development and consequently also on meat production. The myostatin sequence is known in several mammalian species and shows a high degree of amino acid sequence conservation, although the presence of non-silent and silent changes in the coding sequences and several alterations in the introns and untranslated regions have been identified. The objective of our work was to characterize the myostatin coding regions of B. bubalis (Murrah breed) and to compare them with the Bos taurus regions looking for variations in nucleotide and protein sequences. In this way, we were able to identify 12 variations at DNA level and five alterations on the presumed myostatin protein sequence as compared to non double-muscled bovine sequences.

Decoding Delay Minimization in Inter-Session Network Coding

Intra-session network coding has been shown to offer significant gains in terms of achievable throughput and delay in settings where one source multicasts data to several clients. In this paper, we consider a more general scenario where multiple sources transmit data to sets of clients over a wireline overlay network. We propose a novel framework for efficient rate allocation in networks where intermediate network nodes have the opportunity to combine packets from different sources using randomized network coding. We formulate the problem as the minimization of the average decoding delay in the client population and solve it with a gradient-based stochastic algorithm. Our optimized inter-session network coding solution is evaluated in different network topologies and is compared with basic intra-session network coding solutions. Our results show the benefits of proper coding decisions and effective rate allocation for lowering the decoding delay when the network is used by concurrent multicast sessions.

NAMA3DS1-COSPAD1: Subjective video quality assessment database on coding conditions introducing freely available high quality 3D stereoscopic sequences

Research in stereoscopic 3D coding, transmission and subjective assessment methodology depends largely on the availability of source content that can be used in cross-lab evaluations. While several studies have already been presented using proprietary content, comparisons between the studies are difficult since discrepant contents are used. Therefore in this paper, a freely available dataset of high quality Full-HD stereoscopic sequences shot with a semiprofessional 3D camera is introduced in detail. The content was designed to be suited for usage in a wide variety of applications, including high quality studies. A set of depth maps was calculated from the stereoscopic pair. As an application example, a subjective assessment has been performed using coding and spatial degradations. The Absolute Category Rating with Hidden Reference method was used. The observers were instructed to vote on video quality only. Results of this experiment are also freely available and will be presented in this paper as a first step towards objective video quality measurement for 3DTV.