scholarly journals SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments

2014 ◽  
Vol 42 (W1) ◽  
pp. W356-W360 ◽  
Author(s):  
Paolo Di Tommaso ◽  
Giovanni Bussotti ◽  
Carsten Kemena ◽  
Emidio Capriotti ◽  
Maria Chatzou ◽  
...  
Keyword(s):  
Web Server ◽  
Rna Sequence ◽  
Multiple Alignments

scholarly journals A heuristic approach for detecting RNA H-type pseudoknots

2005 ◽  
Vol 21 (17) ◽  
pp. 3501-3508 ◽  
Author(s):  
Chun-Hsiang Huang ◽  
Chin Lung Lu ◽  
Hsien-Tai Chiu
Keyword(s):  
Web Server ◽  
Heuristic Approach ◽  
Biological Processes ◽  
Rna Structures ◽  
Online Analysis ◽  
Rna Sequence ◽  
Associated Functions ◽  
Almost All ◽  
The Web

Abstract Motivation RNA H-type pseudoknots are ubiquitous pseudoknots that are found in almost all classes of RNA and thought to play very important roles in a variety of biological processes. Detection of these RNA H-type pseudoknots can improve our understanding of RNA structures and their associated functions. However, the currently existing programs for detecting such RNA H-type pseudoknots are still time consuming and sometimes even ineffective. Therefore, efficient and effective tools for detecting the RNA H-type pseudoknots are needed. Results In this paper, we have adopted a heuristic approach to develop a novel tool, called HPknotter, for efficiently and accurately detecting H-type pseudoknots in an RNA sequence. In addition, we have demonstrated the applicability and effectiveness of HPknotter by testing on some sequences with known H-type pseudoknots. Our approach can be easily extended and applied to other classes of more general pseudoknots. Availability The web server of our HPknotter is available for online analysis at http://bioalgorithm.life.nctu.edu.tw/HPKNOTTER/ Contact [email protected], [email protected]

scholarly journals RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps

2015 ◽  
Vol 43 (W1) ◽  
pp. W507-W512 ◽  
Author(s):  
Matan Drory Retwitzer ◽  
Maya Polishchuk ◽  
Elena Churkin ◽  
Ilona Kifer ◽  
Zohar Yakhini ◽  
...  
Keyword(s):  
Pattern Matching ◽  
Web Server ◽  
Sequence Structure ◽  
Rna Sequence ◽  
Motif Detection

ON COMPARING TWO STRUCTURED RNA MULTIPLE ALIGNMENTS

2010 ◽  
Vol 08 (06) ◽  
pp. 967-980 ◽  
Author(s):  
VANDANABEN PATEL ◽  
JASON T. L. WANG ◽  
SHEFALI SETIA ◽  
ANURAG VERMA ◽  
CHARLES D. WARDEN ◽  
...  
Keyword(s):  
Dynamic Programming Algorithm ◽  
Web Server ◽  
Pairwise Alignment ◽  
Programming Algorithm ◽  
Multiple Sequence ◽  
Consensus Secondary Structure ◽  
Time Dynamic ◽  
Multiple Alignments ◽  
Alignment Process ◽  
Alignment Result

We present a method, called BlockMatch, for aligning two blocks, where a block is an RNA multiple sequence alignment with the consensus secondary structure of the alignment in Stockholm format. The method employs a quadratic-time dynamic programming algorithm for aligning columns and column pairs of the multiple alignments in the blocks. Unlike many other tools that can perform pairwise alignment of either single sequences or structures only, BlockMatch takes into account the characteristics of all the sequences in the blocks along with their consensus structures during the alignment process, thus being able to achieve a high-quality alignment result. We apply BlockMatch to phylogeny reconstruction on a set of 5S rRNA sequences taken from fifteen bacteria species. Experimental results showed that the phylogenetic tree generated by our method is more accurate than the tree constructed based on the widely used ClustalW tool. The BlockMatch algorithm is implemented into a web server, accessible at . A jar file of the program is also available for download from the web server.

Jurnal uji web serber

2020 ◽  
Author(s):  
Wawan saputra
Keyword(s):  
Web Server ◽  
Word Wide Web

Web server adalah tulang belakang dari word wide web(www)

APLIKASI PENCARI INFORMASI PERMINTAAN LAYANAN WEB YANG ERROR MENGGUNAKAN ALGORITMA BOYER-MOORE

2016 ◽  
Vol 1 (1) ◽  
pp. 001
Author(s):  
Harry Setya Hadi
Keyword(s):  
Data Storage ◽  
Computer Network ◽  
Web Server ◽  
Access Methods ◽  
Ip Address ◽  
String Searching ◽  
Common Process ◽  
Web Server Logs ◽  
Different Parts ◽  
The Web

String searching is a common process in the processes that made the computer because the text is the main form of data storage. Boyer-Moore is the search string from right to left is considered the most efficient methods in practice, and matching string from the specified direction specifically an algorithm that has the best results theoretically. A system that is connected to a computer network that literally pick a web server that is accessed by multiple users in different parts of both good and bad aim. Any activity performed by the user, will be stored in Web server logs. With a log report contained in the web server can help a web server administrator to search the web request error. Web server log is a record of the activities of a web site that contains the data associated with the IP address, time of access, the page is opened, activities, and access methods. The amount of data contained in the resulting log is a log shed useful information.

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