Local Alignment Research Papers - Academia.edu (original) (raw)

In plant, basic leucine zipper (bZIP) transcription factors play various roles in response to biotic and abiotic stimuli, as well as in developmental processes. In the present study, a novel bZIP gene, designated as TabZIP1, was isolated... more

In plant, basic leucine zipper (bZIP) transcription factors play various roles in response to biotic and abiotic stimuli, as well as in developmental processes. In the present study, a novel bZIP gene, designated as TabZIP1, was isolated from wheat leaves infected by Puccinia ...

Polymorphic malware is currently difficult to identify. Such malware is able to mutate into functionally equivalent variants of themselves. Modern detection techniques are not adequate against this rapidly-mutating polymorphic malware.... more

Polymorphic malware is currently difficult to identify. Such malware is able to mutate into functionally equivalent variants of themselves. Modern detection techniques are not adequate against this rapidly-mutating polymorphic malware. The age-old approach of signature-based detection is the only one that has the highest detection rate in real time and is used by almost all antivirus software products. The process of current signature extraction has so far been by manual evaluation. Even the most advanced malware detection process which employs heuristic-based approaches requires progressive evaluation and modification by humans to keep up with new malware variants. The aim of the research reported here is to investigate efficient and effective techniques of string matching algorithm for the automatic identification of some or all new polymorphic malware. We demonstrate how our proposed syntactic-based approach using the well-known string matching Smith-Waterman algorithm can successfully detect the known polymorphic variants of JS.Cassandra virus. Our string-matching approach may revolutionize our understanding of polymorphic variant generation and may lead to a new phase of syntactic-based anti-viral software.

In this paper, a specific method for massive Capillary Elec- trophoresis data analysis based on pattern recognition tech- niques in the wavelet domain is presented. Low-resolution, denoised electropherograms are obtained by applying sev-... more

In this paper, a specific method for massive Capillary Elec- trophoresis data analysis based on pattern recognition tech- niques in the wavelet domain is presented. Low-resolution, denoised electropherograms are obtained by applying sev- eral pre-processing algorithms including discrete wavelet transform, denoising, detection of region of interest and baseline correction. The resultant signal is mapped into multi-character sequences exploiting the first derivative information and multi-level peak height quantization. Next, local alignment algorithms are applied on the coded se- quence for peak pattern recognition. Finally, Gaussian ap- proximation is performed to assure precise peak-height measurements.

Expressed sequence tags (ESTs) were produced from cDNA libraries for immature L1, mature muscle larva and adult stages of the adenophorean nematode Trichinella spiralis. 10,130 ESTs were grouped into 3454 gene clusters. The clusters... more

Expressed sequence tags (ESTs) were produced from cDNA libraries for immature L1, mature muscle larva and adult stages of the adenophorean nematode Trichinella spiralis. 10,130 ESTs were grouped into 3454 gene clusters. The clusters represent a conservative estimate of ...

IgM detection is considered as the gold standard for mumps diagnosis. Currently, most cases in developed countries occur in highly vaccinated populations due to secondary vaccine failure. In these patients, pre-existing vaccine-induced... more

IgM detection is considered as the gold standard for mumps diagnosis. Currently, most cases in developed countries occur in highly vaccinated populations due to secondary vaccine failure. In these patients, pre-existing vaccine-induced antibodies are not able to neutralise the virus, but prevent the typical primary response, so that specific IgM is not always elicited. Consequently, acute infection has to be demonstrated by direct detection of the virus by viral isolation or genomic amplification. RT-PCR allows a diagnosis with the maximum sensitivity to be made and also forms the basis for genotype characterisation by sequencing the SH gene, according to WHO recommendations. However, none of the RT-PCR techniques properly evaluated for the diagnosis of acute mumps infection yields an amplification fragment useful for genotyping, and none of the amplification techniques described for genotyping has proved to be sensitive enough for diagnosis.Development of a RT-PCR for the mumps virus diagnosis and genotyping, properly evaluated in comparison with serological gold-standard technique.195 suspected mumps cases and six wild type MuV genotypes were studied.Our method was able to detect 0.001 TCID50 of mumps virus. Fifty-eight of these showed positive results, of which 54 (93.3%) showed mumps RNA in saliva, while only 20 (34.5%) had mumps IgM in serum. Genotypes G1, G2, H1, H2, D1 and C were identified in positive samples.The technique described could be a very useful tool for mumps surveillance, management and control.

Citation matching is the problem of finding which citation occurs in a given textual corpus. Most existing citation matching work is done on scientific literature. The goal of this paper is to present methods for performing citation... more

Citation matching is the problem of finding which citation occurs in a given textual corpus. Most existing citation matching work is done on scientific literature. The goal of this paper is to present methods for performing citation matching on Sanskrit texts. Exact matching and approximate matching are the two methods for performing citation matching. The exact matching method checks for exact occurrence of the citation with respect to the textual corpus. Approximate matching is a fuzzy string-matching method which computes a similarity score between an individual line of the textual corpus and the citation. The Smith-Waterman-Gotoh algorithm for local alignment, which is generally used in bioinformatics, is used here for calculating the similarity score. This similarity score is a measure of the closeness between the text and the citation. The exact- and approximate-matching methods are evaluated and compared. The methods presented can be easily applied to corpora in other Indic languages like Kannada, Tamil, etc. The approximate-matching method can in particular be used in the compilation of critical editions and plagiarism detection in a literary work.

This paper develops PeSeeD, a new metaheuristic algorithm for finding optimal spaced seed. Sequences matching is a hot topic in bio-informatics, which is used in many applications such as understanding the functional, structural, or... more

This paper develops PeSeeD, a new metaheuristic algorithm for finding optimal spaced seed. Sequences matching is a hot topic in bio-informatics, which is used in many applications such as understanding the functional, structural, or evolutionary relationships between the sequences. The most relevant sequences matching methods are based on seeds designed to match two biological sequences. The first approach which introduced seeds was facilitated via Blastn tool, the approach builds seeds of 11 length size. However, it is clear that not all local alignments have to include an identical fragment of length 11. The spaced seeds approach is one of the methods which does not require a consecutive matching position. Dynamic programming is used to solve this kind of problem and it takes quadratic time. Several approaches have then been proposed to improve the sensitivity of searching in reasonable runtime. To reduce the complexity of such approaches, other heuristics based approaches can als...

Human iris provides a unique structure suitable for non-invasive biometric assessment. The irises are as distinct as fingerprints even for twins. In this paper a robust system for person identification is presented that uses a technique... more

Human iris provides a unique structure suitable for non-invasive biometric assessment. The irises are as distinct as fingerprints even for twins. In this paper a robust system for person identification is presented that uses a technique of localization, alignment, feature extraction, and matching the features of irises. A CASIA iris database has been used to observe the performance of the proposed iris recognition system. The results show that proposed method is quite effective.

Multi-temporal earth-observation imagery is now available at sub-meter accuracy and has been found very useful for performing quick damage detection for urban areas affected by large-scale disasters. The detection of structural damage... more

Multi-temporal earth-observation imagery is now available at sub-meter accuracy and has been found very useful for performing quick damage detection for urban areas affected by large-scale disasters. The detection of structural damage using images taken before and after disaster events is usually modeled as a change detection problem. In this paper, we propose a new perspective for performing change detection, where dissimilarity measures are used to extract urban structural damage. First, image gradient magnitudes ...