NDLI: An Efficient Alignment Algorithm for Searching Simple Pseudoknots over Long Genomic Sequence

Content Provider	ACM Digital Library
Author	Hon, W. K. Wong, Thomas K. F. Ma, Christopher Yiu, S. M. Sadakane, K. Lam, T. W.
Abstract	Structural alignment has been shown to be an effective computational method to identify structural noncoding RNA (ncRNA) candidates as ncRNAs are known to be conserved in secondary structures. However, the complexity of the structural alignment algorithms becomes higher when the structure has pseudoknots. Even for the simplest type of pseudoknots (simple pseudoknots), the fastest algorithm runs in O(mn^3) time, where m, n are the length of the query ncRNA (with known structure) and the length of the target sequence (with unknown structure), respectively. In practice, we are usually given a long DNA sequence and we try to locate regions in the sequence for possible candidates of a particular ncRNA. Thus, we need to run the structural alignment algorithm on every possible region in the long sequence. For example, finding candidates for a known ncRNA of length 100 on a sequence of length 50,000, it takes more than one day. In this paper, we provide an efficient algorithm to solve the problem for simple pseudoknots and it is shown to be 10 times faster. The speedup stems from an effective pruning strategy consisting of the computation of a lower bound score for the optimal alignment and an estimation of the maximum score that a candidate can achieve to decide whether to prune the current candidate or not.
Starting Page	1629
Ending Page	1638
Page Count	10
File Format	PDF
ISSN	15455963
DOI	10.1109/TCBB.2012.104
Volume Number	9
Issue Number	6
Journal	IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2012-11-01
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Bioinformatics,Genomics,RNA,Computational biology,Complexity theory,Algorithm design and analysis,Heuristic algorithms,structural alignment,Noncoding RNAs,pseudoknot
Content Type	Text
Resource Type	Article
Subject	Genetics Biotechnology Applied Mathematics

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

An Efficient Alignment Algorithm for Searching Simple Pseudoknots over Long Genomic Sequence

Memory Efficient Algorithms for Structural Alignment of RNAs with Pseudoknots

Memory Efficient Algorithms for Structural Alignment of RNAs with Pseudoknots

Efficient alignment of rnas with pseudoknots using sequence alignment constraints.

Lifting prediction to alignment of rna pseudoknots

Efficient Parameterized Algorithms for Biopolymer Structure-Sequence Alignment

Bioinformatics original paper sequence analysis pair stochastic tree adjoining grammars for aligning and predicting pseudoknot rna structures (2005).

A memory efficient algorithm for structural alignment of rnas with embedded simple pseudoknots.

Dynamic programming based rna pseudoknot alignment (2009).

An Efficient Alignment Algorithm for Searching Simple Pseudoknots over Long Genomic Sequence

Similar Documents

An Efficient Alignment Algorithm for Searching Simple Pseudoknots over Long Genomic Sequence

Memory Efficient Algorithms for Structural Alignment of RNAs with Pseudoknots

Memory Efficient Algorithms for Structural Alignment of RNAs with Pseudoknots

Efficient alignment of rnas with pseudoknots using sequence alignment constraints.

Lifting prediction to alignment of rna pseudoknots

Efficient Parameterized Algorithms for Biopolymer Structure-Sequence Alignment

Bioinformatics original paper sequence analysis pair stochastic tree adjoining grammars for aligning and predicting pseudoknot rna structures (2005).

A memory efficient algorithm for structural alignment of rnas with embedded simple pseudoknots.

Dynamic programming based rna pseudoknot alignment (2009).

An Efficient Alignment Algorithm for Searching Simple Pseudoknots over Long Genomic Sequence