Abstract:
:One of the most fundamental operations in biological sequence analysis is multiple sequence alignment (MSA). The basic of multiple sequence alignment problems is to determine the most biologically plausible alignments of protein or DNA sequences. In this paper, an alignment method using genetic algorithm for multiple sequence alignment has been proposed. Two different genetic operators mainly crossover and mutation were defined and implemented with the proposed method in order to know the population evolution and quality of the sequence aligned. The proposed method is assessed with protein benchmark dataset, e.g., BALIBASE, by comparing the obtained results to those obtained with other alignment algorithms, e.g., SAGA, RBT-GA, PRRP, HMMT, SB-PIMA, CLUSTALX, CLUSTAL W, DIALIGN and PILEUP8 etc. Experiments on a wide range of data have shown that the proposed algorithm is much better (it terms of score) than previously proposed algorithms in its ability to achieve high alignment quality.
journal_name
EXCLI Jjournal_title
EXCLI journalauthors
Kumar Mdoi
10.17179/excli2015-302subject
Has Abstractpub_date
2015-12-15 00:00:00pages
1232-55issn
1611-2156pii
Doc1232journal_volume
14pub_type
杂志文章相关文献
EXCLI Journal文献大全abstract::Doxorubicin (DOX) is an excellent antineoplastic agent used for the treatment of hematological and solid malignancies. The aqueous extract of Bombyx mori (BMAE) contains amino acids and some flavonoids with obvious cardioprotective effect. The aim of this study was to investigate the possible protective effect of BMAE...
journal_title:EXCLI journal
pub_type: 杂志文章
doi:
更新日期:2014-09-05 00:00:00
abstract::Unlike conventional materials that covalent bonds connecting atoms as the major force to hold the materials together, supramolecular biomaterials rely on noncovalent intermolecular interactions to assemble. The reversibility and biocompatibility of supramolecular biomaterials render them with diverse range of function...
journal_title:EXCLI journal
pub_type: 杂志文章,评审
doi:10.17179/excli2020-2656
更新日期:2020-08-05 00:00:00
abstract::The traditional uses of Portulaca oleracea L. (PO) with anti-inflammatory and anti-cancer activity as well as antioxidants properties were expressed previously. Glioma is considered the most common primary brain tumor and its malignant form is the most lethal adult brain tumor, that glioblastoma covers about 50 % of g...
journal_title:EXCLI journal
pub_type: 杂志文章
doi:10.17179/excli2019-1063
更新日期:2019-03-20 00:00:00
abstract::Lack of data on safety of herbal medicines have endangered human health and life. The present study evaluated the genotoxic and mutagenic effect of Kalanchoe laciniata to access the safety and usefulness of the medicinal plant. Aqua-methanolic and n-hexane extracts of K. laciniata were evaluated for the genotoxic pote...
journal_title:EXCLI journal
pub_type: 杂志文章
doi:10.17179/excli2016-748
更新日期:2017-04-24 00:00:00
abstract::Spontaneous eye-blinks occur much more often than it would be necessary to maintain the tear film on the eyes. Various factors like cognitive demand, task engagement, or fatigue are influencing spontaneous blink rate. During cognitive information processing there is evidence that blinks occur preferably at moments tha...
journal_title:EXCLI journal
pub_type: 杂志文章
doi:10.17179/excli2015-696
更新日期:2015-11-27 00:00:00
abstract::Salmonella enterica serovar Typhi (S. Typhi) is a human restricted pathogen. It biosynthesizes a virulence capsular polysaccharide named as Vi antigen. S. Typhi regulates expression of genes involved in the biosynthesis of Vi antigen in response to osmolarity. Beside Vi-positive isolates, Vi-negative (acapsulated) iso...
journal_title:EXCLI journal
pub_type: 杂志文章
doi:10.17179/excli2014-674
更新日期:2015-02-09 00:00:00
abstract::Bladder cancer (BC) is the sixth most common malignancy in men and 17th in women. Exosomal long non-coding RNAs (lncRNAs) have been defined as a novel biomarker for BC. The aim of this study is to evaluate the clinical significance of urine exosomal PVT-1, ANRIL and PCAT-1 as a biomarker in BC patients with tumors cla...
journal_title:EXCLI journal
pub_type: 杂志文章
doi:10.17179/excli2019-1683
更新日期:2020-03-04 00:00:00
abstract::Curcuminoids are dietary complexes extracted from the seeds of Curcuma longa L. that contain curcumin, bisdemethoxycurcumin and desmethoxycurcumin. Curcuminoids are popular for their pleiotropic therapeutic functions, such as their anti-inflammatory and anti-oxidant effects. Nonetheless, their clinical use is associat...
journal_title:EXCLI journal
pub_type: 杂志文章
doi:10.17179/excli2019-1366
更新日期:2019-06-17 00:00:00
abstract::Serum concentration of lipids and lipoproteins changes during the course of acute coronary syndrome as a consequence of the inflammatory response. The objective of this study was to evaluate the effect of acute myocardial infarction (AMI) on the levels of lipid profile and inflammatory markers. We investigated 400 pat...
journal_title:EXCLI journal
pub_type: 杂志文章
doi:10.17179/excli2014-671
更新日期:2015-04-10 00:00:00
abstract::The aim of this study was to evaluate the effect of acute and chronic physical and psychological stressors on the induction of oxidative stress in male rat liver. Male Wistar rats were randomly divided into 3 groups as following: control, physical and psychological stress groups. Stress was induced by communication bo...
journal_title:EXCLI journal
pub_type: 杂志文章
doi:
更新日期:2014-02-24 00:00:00
abstract::Exposure to microgravity leads to orthostatic intolerance in astronauts and differential vascular structural and functional adaptations have been implicated in its occurrence. The present study tended to clarify the characteristics of vascular inflammation and oxidative stress in hindlimb unweighting (HU) rat vasculat...
journal_title:EXCLI journal
pub_type: 杂志文章
doi:
更新日期:2010-12-23 00:00:00
abstract::The present study deals with the isolation and partial purification of bioactive compounds from the crude methanol extracts of the leaves of Ageratum houstonianum (Asteraceae). The quantification and the identification of compounds in the crude extract and active bands isolated by preparative TLC were accomplished usi...
journal_title:EXCLI journal
pub_type: 杂志文章
doi:
更新日期:2012-02-28 00:00:00
abstract::From both the structural and functional points of view, β-turns play important biological roles in proteins. In the present study, a novel two-stage hybrid procedure has been developed to identify β-turns in proteins. Binary logistic regression was initially used for the first time to select significant sequence param...
journal_title:EXCLI journal
pub_type: 杂志文章
doi:
更新日期:2012-07-05 00:00:00
abstract::Numerous studies have demonstrated the robustness of the framing effect in a variety of contexts, especially in medical decision making. Unfortunately, research is still inconsistent as to how so many variables impact framing effects in medical decision making. Additionally, much attention should be paid to the framin...
journal_title:EXCLI journal
pub_type: 杂志文章
doi:
更新日期:2013-01-18 00:00:00
abstract::To our knowledge, in spite of several trials exploring the beneficial effect of n-3 polyunsaturated fatty acids (PUFA) on polycystic ovary syndrome (PCOS), no comprehensive evidence has investigated the effects of n-3 PUFA consumption on PCOS complications. Therefore, our aim was to conduct a review to investigate the...
journal_title:EXCLI journal
pub_type: 杂志文章,评审
doi:10.17179/excli2019-1534
更新日期:2019-07-25 00:00:00
abstract::Dibutyltin dichloride (DBTC) is an organotin compound used as model for acute and chronic pancreatitis. Oxidative stress is one of the mechanisms of propagation of acinar cell injury in acute pancreatitis. Selenium is an essential cofactor in the antioxidant glutathione peroxidase pathway. Selenium levels are describe...
journal_title:EXCLI journal
pub_type: 杂志文章
doi:10.17179/excli2016-466
更新日期:2017-02-16 00:00:00
abstract::Sleep deprivation affects all aspects of health. Adverse health effects by sleep deviation are still underestimated and undervalued in clinical practice and, to a much greater extent in monitoring human health. We hypothesized that sleep deprivation-induced mild organ injuries; oxidative stress and inflammation might ...
journal_title:EXCLI journal
pub_type: 杂志文章
doi:10.17179/excli2015-245
更新日期:2015-05-18 00:00:00
abstract::A reliable biomarker has not been identified to predict the outcome of traumatic brain injury (TBI) in children. Therefore, the present systematic review and meta-analysis aimed to assess the association between neuron specific enolase (NSE) and traumatic brain injury (TBI) in children. Two independent reviewers searc...
journal_title:EXCLI journal
pub_type: 杂志文章
doi:10.17179/excli2017-405
更新日期:2017-07-03 00:00:00
abstract::To investigate whether offspring sex ratio at birth (SRB) was associated with maternal breast cancer risk, the present case-control study and a meta-analysis of literature were done. A total of 389 female breast cancer patients who had at least one offspring participated in the study. From general population 356 healt...
journal_title:EXCLI journal
pub_type: 杂志文章
doi:
更新日期:2010-07-26 00:00:00
abstract::There are abundant studies indicating that blocking gap junctions (GJs) containing connexin 36 (Cx36) inhibit seizures. However, recent evidences demonstrate proconvulsant effect of such intervention. Electrical coupling between GABAergic interneurons in CA1 region of hippocampus is mediated through Cx36 GJs. We inves...
journal_title:EXCLI journal
pub_type: 杂志文章
doi:
更新日期:2013-03-14 00:00:00
abstract::Metabolic syndrome (MS) is a condition associated with metabolic abnormalities that are characterized by central obesity (e.g. waist circumference or body mass index), hypertension (e.g. systolic or diastolic blood pressure), hyperglycemia (e.g. fasting plasma glucose) and dyslipidemia (e.g. triglyceride and high-dens...
journal_title:EXCLI journal
pub_type: 杂志文章,评审
doi:10.17179/excli2017-911
更新日期:2018-01-10 00:00:00
abstract::The chemical composition of the essential oils of different Allium nigrum L. organs and the antibacterial activity were evaluated. The study is particularly interesting because hitherto there are no reports on the antibacterial screening of this species with specific chemical composition. Therefore, essential oils fro...
journal_title:EXCLI journal
pub_type: 杂志文章
doi:
更新日期:2014-05-13 00:00:00
abstract::Recently, many articles have reported different levels and distribution of amphetamine hitherto detected in biological fluids now appreciably found in aquatic environment at ng/L levels. Identification and measurement of amphetamine and its metabolites in surface and sewage waters using higher performance liquid chrom...
journal_title:EXCLI journal
pub_type: 杂志文章
doi:
更新日期:2011-08-19 00:00:00
abstract::The relationship between leptin, insulin resistance and other hormonal parameters in polycystic ovarian syndrome (PCOS) is controversial. We investigated the effect of metformin on leptin levels in women with PCOS. Thirty women with PCOS received metformin 500 mg thrice a day. After two months of metformin treatment t...
journal_title:EXCLI journal
pub_type: 杂志文章
doi:
更新日期:2011-02-24 00:00:00
abstract::We present the case of a 77 year old male patient with metastatic pancreatic neuroendocrine tumor (NET). The patient was initially treated by extensive surgical resection that however, led to severe complications with delayed recovery. During follow-up, a number of new liver metastases were detected, one of which was ...
journal_title:EXCLI journal
pub_type:
doi:10.17179/excli2019-1220
更新日期:2019-05-21 00:00:00
abstract::Healthcare professionals, especially nurses and pre-hospital emergency (PHE) staff, are influenced by many stressors due to their responsibility to provide comfort as well as care and treatment of patients. The aim of the present study was to identify and rank the occupational stressors in nurses and PHE staff using F...
journal_title:EXCLI journal
pub_type: 杂志文章
doi:10.17179/excli2018-1505
更新日期:2018-08-20 00:00:00
abstract::[This retracts the article DOI: 10.17179/excli2015-642.]. ...
journal_title:EXCLI journal
pub_type: 杂志文章,撤回出版物
doi:10.17179/excli2016-570
更新日期:2016-09-19 00:00:00
abstract::The aim of this study was the design and evaluation of a novel plasma stable, pH-sensitive niosomal formulation of Mitoxantrone by a modified ethanol injection method. Cholesterol hemisuccinate was added instead of cholesterol in order to produce pH-sensitivity property and using PEG-Poly (monomethyl itaconate)-CholC6...
journal_title:EXCLI journal
pub_type: 杂志文章
doi:10.17179/excli2013-609
更新日期:2015-01-06 00:00:00
abstract::Some debates exist regarding the association of diabetes mellitus (DM) with COVID-19 infection severity and mortality. In this study, we aimed to describe and compare the clinical characteristics and outcomes of hospitalized COVID-19 patients with and without DM. In this single-centered, retrospective, observational s...
journal_title:EXCLI journal
pub_type: 杂志文章
doi:10.17179/excli2020-2988
更新日期:2020-11-16 00:00:00
abstract::Oxidative stress is the common underlying mechanism of damage in ischemic stroke. Therefore, we aimed to evaluate the possible protective effects of polyhydroxylated fullerene derivatives on brain infarction and oxidative/nitrosative stress in a rat model of ischemic stroke. The experiment was performed by four groups...
journal_title:EXCLI journal
pub_type: 杂志文章
doi:10.17179/excli2016-309
更新日期:2016-06-20 00:00:00