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PatternHunter: faster and more sensitive homology search

B. Ma, J. Tromp, M. Li
2002 Bioinformatics  
Results: We present a new homology search algorithm 'PatternHunter' that uses a novel seed model for increased sensitivity and new hit-processing techniques for significantly increased speed.  ...  Motivation: Genomics and proteomics studies routinely depend on homology searches based on the strategy of finding short seed matches which are then extended.  ...  He also brought Buhler (2001) and Indyk et al. (1998) to our attention. We thank Larry Miller for working on related projects, David Lipman for comments and bringing Califano and Rigoutsos (1995)  ... 
doi:10.1093/bioinformatics/18.3.440 pmid:11934743 fatcat:5p36zzrtp5fmhd4haozbrqb5xa

PATTERNHUNTER II: HIGHLY SENSITIVE AND FAST HOMOLOGY SEARCH

MING LI, BIN MA, DEREK KISMAN, JOHN TROMP
2004 Journal of Bioinformatics and Computational Biology  
At Blastn speed, PatternHunter II approaches Smith-Waterman sensitivity, bringing homology search technology back to a full circle.  ...  homology search.  ...  Using optimized multiple spaced seeds, PatternHunter II is over a thousand times faster than Smith-Waterman at approximately the same sensitivity, for DNA sequence search.  ... 
doi:10.1142/s0219720004000661 pmid:15359419 fatcat:qr3tj7acp5f3dnzdk7nratdcaq

Good spaced seeds for homology search

K. P. Choi, F. Zeng, L. Zhang
2004 Bioinformatics  
Since homologous sequences may have diverse similarity, we assess the sensitivity of spaced seeds over a range of similarity levels and present a list of good spaced seeds for facilitating homology search  ...  We validate that the listed spaced seeds are indeed more sensitive using three arbitrarily chosen pairs of DNA genomic sequences.  ...  Li for graciously providing us the PatternHunter program, J. Buhler for the Mandala package, Z. Zhang for helpful discussions, and Z. Wang for assistance in PatternHunter.  ... 
doi:10.1093/bioinformatics/bth037 pmid:14764573 fatcat:f5tc6ihgdne5lolcuv5medjdsy

A TUTORIAL OF RECENT DEVELOPMENTS IN THE SEEDING OF LOCAL ALIGNMENT

DANIEL G. BROWN, MING LI, BIN MA
2004 Journal of Bioinformatics and Computational Biology  
We begin with a review of classical methods and early heuristic methods, and then focus on more recent work on the seeding of local alignment.  ...  We show that these techniques give a vast improvement in both sensitivity and specificity over previous methods, and can achieve sensitivity at the level of classical algorithms while requiring orders  ...  , and the Human Frontier Science Program.  ... 
doi:10.1142/s0219720004000983 pmid:15617167 fatcat:gabobgqu5ffutgh6rd4itgpiyu

DNACompress: fast and effective DNA sequence compression

X. Chen, M. Li, B. Ma, J. Tromp
2002 Bioinformatics  
ACKNOWLEDGEMENTS XC and ML was supported by NSF ITR grant 0085801. JT was supported by BSI.  ...  PatternHunter does homology search like Blastn, but with many innovations improving sensitivity, alignments, memory use, and speed.  ...  deferred at the end of PatternHunter homology search.  ... 
doi:10.1093/bioinformatics/18.12.1696 pmid:12490460 fatcat:ivfxsqrsmncfxpmll2ssf5kv4a

HOMOLOGY SEARCH METHODS [chapter]

Daniel G. Brown, Ming Li, Bin Ma
2004 The Practical Bioinformatician  
For example, the optimal spaced seeds of PatternHunter increase speed and sensitivity.  ...  As data sets grew, faster but less sensitive heuristic algorithms, such as FASTA and BLAST, became a dominant force in the late 1980s and 1990s.  ...  , and the Human Frontier Science Program.  ... 
doi:10.1142/9789812562340_0010 fatcat:zphjhrcsfbb2vh5cwxescb6fba

OPTIMAL SPACED SEEDS FOR HOMOLOGOUS CODING REGIONS

BROŇA BREJOVÁ, DANIEL G. BROWN, TOMÁŠ VINAŘ
2004 Journal of Bioinformatics and Computational Biology  
Our results offer the hope of improved gene finding due to fewer missed exons in DNA/DNA comparison, and more effective homology search in general, and may have applications outside of bioinformatics.  ...  Such seeds have been used before in the program PatternHunter, and have given improved sensitivity and running time relative to BLASTN in genome-genome comparison.  ...  (http://www.BioinformaticsSolutions.com/) for providing us with a version of PatternHunter customized to our needs and Ming Li for providing access to the manuscript of Keich et al. 4  ... 
doi:10.1142/s0219720004000326 pmid:15290755 fatcat:5j55bubcwbeflpql7zgceqq4bu

A Filtering Algorithm for Efficient Retrieving of DNA Sequence

M. Nordin A. Rahman, M. Yazid M. Saman, Aziz Ahmad, A. Osman M. Tap
2009 Journal of clean energy technologies  
This task becomes more complex and challenging as the sizes of public sequence databases get very large and are increasing exponentially each year.  ...  DNA sequence similarity search is an important task in computational biology applications. Similarity search procedure is executed by an alignment process between query and targeted sequences.  ...  To increase the sensitivity in homology search, PatternHunter II increases the number of seeds and reduces the weight of a single seed [10] .  ... 
doi:10.7763/ijcte.2009.v1.16 fatcat:hjbt5el2frgaho6yenaukpptdq

On half gapped seed

Wei Chen, Wing-kin Sung
2003 Genome Informatics Series  
sensitivity and efficiency.  ...  In this paper, we proposed a new type of seed for Blast-like homology search tools called "half seed".  ...  Finding faster and more sensitive methods for homology search has attracted a lot of research works. The first solution to the homology search problem is contributed by Smith and Waterman [11] .  ... 
pmid:15706532 fatcat:wpccbbyv5nfyjisdee6pe5lyne

On Half Gapped Seed

Wei Chen, Wing-kin Sung
2003 Genome Informatics Series  
In this paper, we proposed a new type of seed for Blast-like homology search tools called"half seed".  ...  When compared with the"gapped seed", which is proposed together with a new Blast-like searching tool, PatternHunter, this new seed offers a much wider range of choices for performing tradeoff between sensitivity  ...  Finding faster and more sensitive methods for homology search has attracted a lot of research works . The first solution to the homology search problem is contributed by Smith and Waterman [11] .  ... 
doi:10.11234/gi1990.14.176 fatcat:bzcrbfzhpfapzot6gkmrzgkusa

Improving the Sensitivity and Specificity of Protein Homology Search by Incorporating Predicted Secondary Structures [chapter]

Bin Ma, Lieyu Wu, Kaizhong Zhang
2005 Lecture Notes in Computer Science  
In this paper, we improve the homology search performance by the combination of the predicted protein secondary structures and protein sequences.  ...  Previous research suggested that the straightforward combination of predicted secondary structures did not improve the homology search performance, mostly because the errors in the structure prediction  ...  Acknowledgment This research was undertaken, in part, thanks to funding from NSERC, PREA, and the Canada Research Chairs Program. We thank Dr.  ... 
doi:10.1007/11428848_122 fatcat:ayqkkuwxdjacndrmxf3vnxzwfq

Vector seeds: An extension to spaced seeds

Broňa Brejová, Daniel G. Brown, Tomáš Vinař
2005 Journal of computer and system sciences (Print)  
We present improved techniques for finding homologous regions in DNA and protein sequences.  ...  between homologous coding DNA sequences.  ...  and Information Technology Ontario, and by Ontario Graduate Scholarships.  ... 
doi:10.1016/j.jcss.2004.12.008 fatcat:45akqpukc5gkfjj2tngiimmaom

Homology search for genes

Xuefeng Cui, Tomáš Vinař, Broňa Brejová, Dennis Shasha, Ming Li
2007 Computer applications in the biosciences : CABIOS  
Compared to traditional homology search, our novel approach identifies splice sites much more reliably and can even locate exons that were lost in the query gene.  ...  To find such genes, homology search tools, such as BLAST or PatternHunter, return a set of high-scoring pairs (HSPs).  ...  The focus of the field is on designing faster and more sensitive methods to search for sequences similar to a query DNA or protein sequence in one or more huge databases [see, e.g.  ... 
doi:10.1093/bioinformatics/btm225 pmid:17646351 fatcat:yltevtnalbhrti2bwko4vjwpka

rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison

Lars Hahn, Chris-André Leimeister, Rachid Ounit, Stefano Lonardi, Burkhard Morgenstern, Andreas Prlic
2016 PLoS Computational Biology  
We show that, for database searching, rasbhari generates pattern sets with slightly higher sensitivity than existing approaches.  ...  We propose a modified hill-climbing algorithm to optimize pattern sets for database searching, read mapping and alignment-free sequence comparison of nucleic-acid sequences; our implementation of this  ...  Acknowledgments We would like to thank Laurent Noé for helpful discussions and for pointing out the similarity between the overlap complexity and the variance of the number of spaced-word matches.  ... 
doi:10.1371/journal.pcbi.1005107 pmid:27760124 pmcid:PMC5070788 fatcat:wi7dcyps4jfjzb6gams4swt6ji

Multiple spaced seeds for homology search

L. Ilie, S. Ilie
2007 Bioinformatics  
The introduction of optimal spaced seeds in PatternHunter, (Ma et al., 2002) , has increased both the sensitivity and the speed of homology search and it has been adopted by many alignment programs such  ...  Motivation: Homology search finds similar segments between two biological sequences, such as DNA or protein sequences.  ...  Acknowledgements We thank Ming Li (Li, 2007) and Bin Ma (Ma, 2007) for kindly providing the sensitivities of their seeds in .  ... 
doi:10.1093/bioinformatics/btm422 pmid:17804438 fatcat:zdzcczsp25cq3ixux6dghrwfqe
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