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Designing seeds for similarity search in genomic DNA
2005
Journal of computer and system sciences (Print)
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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
2003
Proceedings of the seventh annual international conference on Computational molecular biology - RECOMB '03
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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
2004
Proceedings of the eighth annual international conference on Computational molecular biology - RECOMB '04
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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
2005
Journal of Computational Biology
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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
2014
Nucleic Acids Research
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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
2004
Bioinformatics
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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
2017
BMC Genomics
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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
2006
BMC Bioinformatics
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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
2004
Genome Research
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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
2012
BMC Bioinformatics
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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]
2020
arXiv
pre-print
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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
2020
Bioinformatics
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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
2010
BMC Genomics
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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
2011
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine - BCB '11
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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
2011
PLoS ONE
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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
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