Informs Journal on Computing最新文献

筛选

英文中文

Least-Squares Support Vector Machine Approach to Viral Replication Origin Prediction. 病毒复制起源预测的最小二乘支持向量机方法。

IF 2.1 4区计算机科学

Informs Journal on Computing Pub Date : 2010-06-01 DOI: 10.1287/ijoc.1090.0360

Raul Cruz-Cano, David S H Chew, Choi Kwok-Pui, Leung Ming-Ying

{"title":"Least-Squares Support Vector Machine Approach to Viral Replication Origin Prediction.","authors":"Raul Cruz-Cano, David S H Chew, Choi Kwok-Pui, Leung Ming-Ying","doi":"10.1287/ijoc.1090.0360","DOIUrl":"https://doi.org/10.1287/ijoc.1090.0360","url":null,"abstract":"Replication of their DNA genomes is a central step in the reproduction of many viruses. Procedures to find replication origins, which are initiation sites of the DNA replication process, are therefore of great importance for controlling the growth and spread of such viruses. Existing computational methods for viral replication origin prediction have mostly been tested within the family of herpesviruses. This paper proposes a new approach by least-squares support vector machines (LS-SVMs) and tests its performance not only on the herpes family but also on a collection of caudoviruses coming from three viral families under the order of caudovirales. The LS-SVM approach provides sensitivities and positive predictive values superior or comparable to those given by the previous methods. When suitably combined with previous methods, the LS-SVM approach further improves the prediction accuracy for the herpesvirus replication origins. Furthermore, by recursive feature elimination, the LS-SVM has also helped find the most significant features of the data sets. The results suggest that the LS-SVMs will be a highly useful addition to the set of computational tools for viral replication origin prediction and illustrate the value of optimization-based computing techniques in biomedical applications.","PeriodicalId":13620,"journal":{"name":"Informs Journal on Computing","volume":"22 3","pages":"457-470"},"PeriodicalIF":2.1,"publicationDate":"2010-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1287/ijoc.1090.0360","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29204186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 8

Palindromes in SARS and Other Coronaviruses. SARS 和其他冠状病毒中的倒位基因

IF 2.1 4区计算机科学

Informs Journal on Computing Pub Date : 2004-01-01 DOI: 10.1287/ijoc.1040.0087

David S H Chew, Kwok Pui Choi, Hans Heidner, Ming-Ying Leung

{"title":"Palindromes in SARS and Other Coronaviruses.","authors":"David S H Chew, Kwok Pui Choi, Hans Heidner, Ming-Ying Leung","doi":"10.1287/ijoc.1040.0087","DOIUrl":"10.1287/ijoc.1040.0087","url":null,"abstract":"With the identification of a novel coronavirus associated with the severe acute respiratory syndrome (SARS), computational analysis of its RNA genome sequence is expected to give useful clues to help elucidate the origin, evolution, and pathogenicity of the virus. In this paper, we study the collective counts of palindromes in the SARS genome along with all the completely sequenced coronaviruses. Based on a Markov-chain model for the genome sequence, the mean and standard deviation for the number of palindromes at or above a given length are derived. These theoretical results are complemented by extensive simulations to provide empirical estimates. Using a z score obtained from these mathematical and empirical means and standard deviations, we have observed that palindromes of length four are significantly underrepresented in all the coronaviruses in our data set. In contrast, length-six palindromes are significantly underrepresented only in the SARS coronavirus. Two other features are unique to the SARS sequence. First, there is a length-22 palindrome TCTTTAACAAGCTTGTTAAAGA spanning positions 25962-25983. Second, there are two repeating length-12 palindromes TTATAATTATAA spanning positions 22712-22723 and 22796-22807. Some further investigations into possible biological implications of these palindrome features are proposed.","PeriodicalId":13620,"journal":{"name":"Informs Journal on Computing","volume":"16 4","pages":"331-340"},"PeriodicalIF":2.1,"publicationDate":"2004-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4066412/pdf/nihms583805.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32455561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0