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Fold recognition by combining profile–profile alignment and support vector machine
Han, Sangjo,Lee, Byung-chul,Yu, Seung Taek,Jeong, Chan-seok,Lee, Soyoung,Kim, Dongsup Oxford University Press 2005 Bioinformatics Vol.21 No.11
<P><B>Motivation:</B> Currently, the most accurate fold-recognition method is to perform profile–profile alignments and estimate the statistical significances of those alignments by calculating <I>Z</I>-score or <I>E</I>-value. Although this scheme is reliable in recognizing relatively close homologs related at the family level, it has difficulty in finding the remote homologs that are related at the superfamily or fold level.</P><P><B>Results:</B> In this paper, we present an alternative method to estimate the significance of the alignments. The alignment between a query protein and a template of length <I>n</I> in the fold library is transformed into a feature vector of length <I>n</I> + 1, which is then evaluated by support vector machine (SVM). The output from SVM is converted to a posterior probability that a query sequence is related to a template, given SVM output. Results show that a new method shows significantly better performance than PSI-BLAST and profile–profile alignment with <I>Z</I>-score scheme. While PSI-BLAST and <I>Z</I>-score scheme detect 16 and 20% of superfamily-related proteins, respectively, at 90% specificity, a new method detects 46% of these proteins, resulting in more than 2-fold increase in sensitivity. More significantly, at the fold level, a new method can detect 14% of remotely related proteins at 90% specificity, a remarkable result considering the fact that the other methods can detect almost none at the same level of specificity.</P><P><B>Contact:</B> kds@kaist.ac.kr</P>
AtRTPrimer: database for Arabidopsis genome-wide homogeneous and specific RT-PCR primer-pairs
Han, Sangjo,Kim, Dongsup BioMed Central 2006 BMC bioinformatics Vol.7 No.-
<P><B>Background</B></P><P>Primer design is a critical step in all types of RT-PCR methods to ensure specificity and efficiency of a target amplicon. However, most traditional primer design programs suggest primers on a single template of limited genetic complexity. To provide researchers with a sufficient number of pre-designed specific RT-PCR primer pairs for whole genes in Arabidopsis, we aimed to construct a genome-wide primer-pair database.</P><P><B>Description</B></P><P>We considered the homogeneous physical and chemical properties of each primer (homogeneity) of a gene, non-specific binding against all other known genes (specificity), and other possible amplicons from its corresponding genomic DNA or similar cDNAs (additional information). Then, we evaluated the reliability of our database with selected primer pairs from 15 genes using conventional and real time RT-PCR.</P><P><B>Conclusion</B></P><P>Approximately 97% of 28,952 genes investigated were finally registered in <I>AtRTPrimer</I>. Unlike other freely available primer databases for <I>Arabidopsis thaliana</I>, <I>AtRTPrimer </I>provides a large number of reliable primer pairs for each gene so that researchers can perform various types of RT-PCR experiments for their specific needs. Furthermore, by experimentally evaluating our database, we made sure that our database provides good starting primer pairs for Arabidopsis researchers to perform various types of RT-PCR experiments.</P>
한상조(Sangjo Han),서정민(JeongMin Seo),최범석(Bum Seog Choi),박준영(Jun-Young Park) 대한기계학회 2011 대한기계학회 춘추학술대회 Vol.2011 No.10
Recently renewable energy gets a lot of attention to generate electricity. One of them is Ocean Thermal Energy Conversion (OTEC). OTEC system provides the high pressure working fluid to the turbine-generator and produce electricity. However, small temperature difference in seawater requires the turbine design with high efficiency. The paper presents the details of 20kW turbine development for CC-OTEC including the thermal cycle analysis and meridional design of the 20kW turbine for CC-OTEC.
한상조(Sangjo Han),최범석(Bum Seog Choi),박무룡(Moo Ryong Park) 대한기계학회 2010 대한기계학회 춘추학술대회 Vol.2010 No.11
The paper discusses the development of hydrogen liquefaction turbine. Hydrogen gas has good energy density by weight, but has poor energy density compared with hydrocarbons. To get same energy with hydrocarbon, hydrogen needs large storage tanks. Liquefaction of hydrogen can solve this problem. In Claude cycle, the liquefaction system requires a turbo-expander which is not developed domestically. This research covers the process of developing the hydrogen liquefaction turbo-expander from meridional designs to 3D CFD. Off-design performance is checked in different rotating speed and expansion ratio. To check the performance of the turbo-expander, 3D fully CFD simulation is conducted to check the flow and thermal performance using ANSYS CFX. Due to high expansion ratio(5) required for a hydrogen liquefaction system, multi-stage design is employed in this study.
한상조(Sangjo Han),김치하(Cheeha Kim) 한국정보과학회 1998 정보과학회논문지 : 시스템 및 이론 Vol.25 No.11
유선망과 기지국을 가지지 않는 이동 호스트로만 구성된 Ad-Hoc 망에서는 호스트간의 경로수정이 자주 요구되므로 경로설정이 중요한 문제이다. 이전의 대부분의 방법들은 모든 이동 호스트를 동일한 라우터로 보고 유선망에서의 경로설정방법을 적용한다. 그러나 Ad-Hoc 망은 사용가능 대역폭, 망 구성형태 변화정도, 라우터 수와 기능, 호스트의 능력등이 유선망과는 근본적으로 다르다. 따라서 빈번한 경로 변화는 통신 오버헤드와 경로설정 지연시간을 증가시키는 문제를 발생한다. 이 논문에서는 이러한 문제를 해결하기 위하여 Ad-Hoc 망의 특성을 고려하는 경로설정 방법을 제안한다. 제안한 방법에서는 호스트들을 클러스터로 묶어 경로설정 기능을 차별화하며 클러스터의 헤드가 지역적인 망 토폴로지를 유지하고 경로 설정과 재설정을 지원하는 계층적인 경로설정 방법을 사용하여 통신오버헤드와 패킷지연을 줄였다. 제안한 방법의 성능을 평가하기 위하여 모의실험을 통하여 기존의 대표적인 방법들과 통신오버헤드와 패킷지연 측면에서 비교하였으며 특히 호스트의 이동특성이 서로 다른 경우에 매우 우수한 결과를 보였다. Routing is an important issue in Ad-Hoc mobile networks which consist of mobile hosts without the reliable network infrastructure such as a wired backbone and base stations, because route updates are frequently required to adapt the routes to wireless link changes In previous works, most of the routing schemes are based on the routing protocols in wired networks and operate all mobile hosts as identical routers. But Ad-Hoc networks are intrinsically different from wired networks in available bandwidth, topology change rate, number of routers, routing function and host capability. Frequent route updates in previous schemes cause more communication overhead and rerouting delay. In this paper, we propose a routing scheme considering the Ad-Hoc network environment to resolve these problems in Ad-Hoc mobile networks Our scheme reduces communication overhead and rerouting delay using a hierarchical routing approach. The cluster heads maintain the cluster topology and the local network topology, and support routing and rerouting. We present a profile based clustering algorithm, a new metric to determine a proper route, connection less/oriented routing procedures, and cluster topology update procedure. We simulate our proposed routing scheme and the previous schemes for the performance comparison, and present the results. Compared with previous schemes, our proposed routing scheme has lower communication overhead and packet delay in a heterogeneous mobile environment.