Filters








84,031 Hits in 4.1 sec

Designing seeds for similarity search in genomic DNA

Jeremy Buhler, Uri Keich, Yanni Sun
2005 Journal of computer and system sciences (Print)  
Large-scale comparisons of genomic DNA are of fundamental importance in annotating functional elements in genomes.  ...  We also describe Mandala, a software tool for seed design, and show that it can be used to improve the sensitivity of alignment in practice.  ...  of seeds; and Steven Altschul and Alejandro Schäffer, for helpful suggestions on the design of Mandala.  ... 
doi:10.1016/j.jcss.2004.12.003 fatcat:g74u6hvngjgcnfwmouce3taobu

Designing seeds for similarity search in genomic DNA

Jeremy Buhler, Uri Keich, Yanni Sun
2003 Proceedings of the seventh annual international conference on Computational molecular biology - RECOMB '03  
Large-scale comparisons of genomic DNA are of fundamental importance in annotating functional elements in genomes.  ...  We also describe Mandala, a software tool for seed design, and show that it can be used to improve the sensitivity of alignment in practice.  ...  of seeds; and Steven Altschul and Alejandro Schäffer, for helpful suggestions on the design of Mandala.  ... 
doi:10.1145/640075.640083 dblp:conf/recomb/BuhlerKS03 fatcat:vs7o3cgzfbfl5iygmoqzconyte

Designing multiple simultaneous seeds for DNA similarity search

Yanni Sun, Jeremy Buhler
2004 Proceedings of the eighth annual international conference on Computational molecular biology - RECOMB '04  
The challenge of similarity search in massive DNA sequence databases has inspired major changes in BLAST-style alignment tools, which accelerate search by inspecting only pairs of sequences sharing a common  ...  Some of these changes raise the possibility of improving search performance by probing sequence pairs with several distinct seeds, any one of which is sufficient for a seed match.  ...  Our multi-seed designs are good candidates for inclusion in indexing-and hardware-based similarity search tools.  ... 
doi:10.1145/974614.974625 dblp:conf/recomb/SunB04 fatcat:dmhrhdcyyjelfk42u3wjyoljmi

Designing Multiple Simultaneous Seeds for DNA Similarity Search

Yanni Sun, Jeremy Buhler
2005 Journal of Computational Biology  
The challenge of similarity search in massive DNA sequence databases has inspired major changes in BLAST-style alignment tools, which accelerate search by inspecting only pairs of sequences sharing a common  ...  Some of these changes raise the possibility of improving search performance by probing sequence pairs with several distinct seeds, any one of which is sufficient for a seed match.  ...  Our multi-seed designs are good candidates for inclusion in indexing-and hardware-based similarity search tools.  ... 
doi:10.1089/cmb.2005.12.847 pmid:16108721 fatcat:ym6sy3we6fcovpsfyp5g7hih5m

Improved search heuristics find 20 000 new alignments between human and mouse genomes

Martin C. Frith, Laurent Noé
2014 Nucleic Acids Research  
This study designs and tests seeding methods for inter-mammal and inter-insect genome comparison.  ...  Sequence similarity search is a fundamental way of analyzing nucleotide sequences.  ...  ACKNOWLEDGEMENTS We are especially grateful to LASTZ author Bob Harris for implementing allowBackToBackGaps and making valuable comments on the manuscript.  ... 
doi:10.1093/nar/gku104 pmid:24493737 pmcid:PMC3985675 fatcat:7omwbdhm2ncanjo6b7cyq22t34

Good spaced seeds for homology search

K. P. Choi, F. Zeng, L. Zhang
2004 Bioinformatics  
in DNA genomic sequences.  ...  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  ...  Buhler for the Mandala package, Z. Zhang for helpful discussions, and Z. Wang for assistance in PatternHunter. This work is partially supported by BMRC Research Grant BMRC01/1/21/19/140.  ... 
doi:10.1093/bioinformatics/bth037 pmid:14764573 fatcat:f5tc6ihgdne5lolcuv5medjdsy

Whole genome analysis of CRISPR Cas9 sgRNA off-target homologies via an efficient computational algorithm

Hong Zhou, Michael Zhou, Daisy Li, Joseph Manthey, Ekaterina Lioutikova, Hong Wang, Xiao Zeng
2017 BMC Genomics  
A highly efficient computationl algorithm was developed for whole genome sgRNA design and off-target homology searches.  ...  Conclusions: By means of the novel and efficient sgRNA homology search algorithm introduced in this article, genome wide sgRNA design and off-target analysis were conducted and the results confirmed the  ...  Furthermore, we also assume that human genome has exactly three billion 23-base regions for sgRNA offtarget search on one DNA strand.  ... 
doi:10.1186/s12864-017-4225-1 pmid:29219081 pmcid:PMC5773898 fatcat:pppq6kdm5jg2bfza3mjikxletm

Choosing the best heuristic for seeded alignment of DNA sequences

Yanni Sun, Jeremy Buhler
2006 BMC Bioinformatics  
Seeded alignment is an important component of algorithms for fast, large-scale DNA similarity search.  ...  For each seed type, we use an extended version of our Mandala seed design software to choose seeds with optimized sensitivity for various levels of specificity.  ...  Acknowledgements We thank our anonymous referees for many helpful suggestions to improve the manuscript. This work was supported by NSF CAREER Grant DBI-0237903.  ... 
doi:10.1186/1471-2105-7-133 pmid:16533404 pmcid:PMC1468433 fatcat:jjvxv7querb3zkqxt3jx6zjsne

An ORFeome-based Analysis of Human Transcription Factor Genes and the Construction of a Microarray to Interrogate Their Expression

D. N. Messina
2004 Genome Research  
Because the HMM used in our Pfam search used a relatively low cutoff for motif similarities, we expected to also detect false positives by this route. To Figure 1 Creation of the seed set.  ...  By using the seed set of 1468 known human TF genes, we searched ScriptSure, a representation of the human transcriptome, using two methods: a high-stringency BLASTN search and an hmmpfam search for DNA-binding  ... 
doi:10.1101/gr.2584104 pmid:15489324 pmcid:PMC528918 fatcat:x3kqe5m3mjachbv3rztuiboiyq

Genome-scale NCRNA homology search using a Hamming distance-based filtration strategy

Yanni Sun, Osama Aljawad, Jikai Lei, Alex Liu
2012 BMC Bioinformatics  
The experimental results demonstrate that a carefully designed Hamming distance seed can achieve better sensitivity in searching for poorly conserved ncRNAs than conventional sequence comparison tools.  ...  Conclusions: Hamming distance seeds provide better sensitivity as a filtration strategy for genome-wide ncRNA homology search than the existing seeding strategies used in BLAST-like tools.  ...  Acknowledgements This work was supported, in part, by the NSF CAREER Grant DBI-0953738. This article has been published as part of BMC Bioinformatics  ... 
doi:10.1186/1471-2105-13-s3-s12 pmid:22536896 pmcid:PMC3311100 fatcat:m7i2p2utwvfarnk52sdjr244be

Read Mapping Near Non-Volatile Memory [article]

S. Karen Khatamifard, Zamshed Chowdhury, Nakul Pande, Meisam Razaviyayn, Chris Kim, Ulya R. Karpuzcu
2020 arXiv   pre-print
However, the excessive energy consumption and lack of support for similarity matching (under NGS and genomic variation induced noise) renders direct application of TCAM infeasible, irrespective of volatility  ...  Besides genomic variations, NGS imperfections induce noise in reads.  ...  Designed for similarity search (in the presence of NGS or genomic variation triggered noise), GeNVoM's non-volatile TCAM arrays can directly handle substitutions, by construction (Sect. 3.3).  ... 
arXiv:1709.02381v3 fatcat:zbslwnctgbegbkl7mpj5ta5tim

Minimally-overlapping words for sequence similarity search

Martin C Frith, Laurent Noé, Gregory Kucherov
2020 Bioinformatics  
Analysis of genetic sequences is usually based on finding similar parts of sequences, e.g. DNA reads and/or genomes.  ...  For huge data, sparse seeding is useful, where we only consider seeds at a subset of positions in a sequence.  ...  Acknowledgments We are grateful to Paul Horton for suggesting seeds starting with a, and Shotaro Tadachi for investigating word-free tracts in human DNA.  ... 
doi:10.1093/bioinformatics/btaa1054 pmid:33346833 pmcid:PMC8016470 fatcat:xqpza3zvcvernfnmwza3texrfu

Using paired-end sequences to optimise parameters for alignment of sequence reads against related genomes

Abhirami Ratnakumar, Sean McWilliam, Wesley Barris, Brian P Dalrymple
2010 BMC Genomics  
A range of different search parameters, with a particular focus on contiguous and discontiguous seeds, were used for each program.  ...  Of the programs tested, MegaBLAST with short contiguous seed lengths (word size 8-11) performed best in this particular task.  ...  Sheep Genomics Consortium (ISGC), in particular John McEwan and James Kijas for useful discussions.  ... 
doi:10.1186/1471-2164-11-458 pmid:20678236 pmcid:PMC3091654 fatcat:sqzvybc3pfchvb3an77bqhgn5i

NcRNA homology search using Hamming distance seeds

Osama Aljawad, Yanni Sun, Alex Liu, Jikai Lei
2011 Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine - BCB '11  
Our experiments demonstrate that the carefully designed Hamming distance seed can achieve better sensitivity in searching for poorly conserved ncRNAs than conventional sequence comparison tools.  ...  Existing genome-scale ncRNA homology search tools identify ncRNAs in local sequence alignments generated by conventional sequence comparison methods.  ...  Acknowledgments This work was supported, in part, by the NSF CAREER Grant DBI-0953738.  ... 
doi:10.1145/2147805.2147828 dblp:conf/bcb/AljawadSLL11 fatcat:zjxkmu5hbfd6hkombunjrjwa5e

SEAS: A System for SEED-Based Pathway Enrichment Analysis

Xizeng Mao, Yu Zhang, Ying Xu, Vladimir Brusic
2011 PLoS ONE  
We present here a computational tool, SEAS, for pathway enrichment analysis over a given set of genes in a specified organism against the pathways (or subsystems) in the SEED database, a popular pathway  ...  database for bacteria.  ...  Author Contributions Conceived and designed the experiments: YX XM. Performed the experiments: XM YZ. Analyzed the data: XM YZ. Wrote the paper: XM YX.  ... 
doi:10.1371/journal.pone.0022556 pmid:21799897 pmcid:PMC3142180 fatcat:vgoqqkj6qreftigfm5sqixcs2q
« Previous Showing results 1 — 15 out of 84,031 results