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Multiple filtration and approximate pattern matching
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/spe.4380180407openalex-snapshot
Fast approximate string matching
inferredcites →https://doi.org/10.1007/3-540-52846-6_103openalex-snapshot
Boyer-Moore approach to approximate string matching
inferredcites →https://doi.org/10.1007/3-540-56024-6_15openalex-snapshot
Fast and practical approximate string matching
inferredcites →https://doi.org/10.1007/bf01185432openalex-snapshot
A sublinear algorithm for approximate keyword searching
inferredcites →https://doi.org/10.1016/0016-0032(58)90688-4openalex-snapshot
An introduction to probability theory and its applications
inferredcites →https://doi.org/10.1016/0020-0190(89)90188-9openalex-snapshot
Simple and efficient string matching with k mismatches
inferredcites →https://doi.org/10.1016/0020-0190(94)00032-8openalex-snapshot
An algorithm for approximate membership checking with application to password security
inferredcites →https://doi.org/10.1016/0022-0000(83)90002-8openalex-snapshot
Time-space-optimal string matching
inferredcites →https://doi.org/10.1016/0166-218x(88)90076-5openalex-snapshot
A new distance metric on strings computable in linear time
inferredcites →https://doi.org/10.1016/0196-6774(85)90023-9openalex-snapshot
Finding approximate patterns in strings
inferredcites →https://doi.org/10.1016/0196-6774(89)90010-2openalex-snapshot
Fast parallel and serial approximate string matching
inferredcites →https://doi.org/10.1016/0304-3975(86)90178-7openalex-snapshot
Efficient string matching with k mismatches
inferredcites →https://doi.org/10.1016/0304-3975(87)90042-9openalex-snapshot
Parallel string matching with k mismatches
inferredcites →https://doi.org/10.1016/0304-3975(92)90138-6openalex-snapshot
An approximate string-matching algorithm
inferredcites →https://doi.org/10.1016/0304-3975(92)90143-4openalex-snapshot
Approximate string-matching with q-grams and maximal matches
inferredcites →https://doi.org/10.1016/0885-064x(88)90008-8openalex-snapshot
Data structures and algorithms for approximate string matching
inferredcites →https://doi.org/10.1070/im1985v024n03abeh001245openalex-snapshot
RECOGNITION OF AN APPROXIMATE OCCURRENCE OF WORDS ON A TURING MACHINE IN REAL TIME
inferredcites →https://doi.org/10.1073/pnas.78.12.7665openalex-snapshot
Enhanced graphic matrix analysis of nucleic acid and protein sequences.
inferredcites →https://doi.org/10.1073/pnas.80.3.726openalex-snapshot
Rapid similarity searches of nucleic acid and protein data banks.
inferredcites →https://doi.org/10.1073/pnas.83.14.5155openalex-snapshot
A measure of the similarity of sets of sequences not requiring sequence alignment.
inferredcites →https://doi.org/10.1090/s0025-5718-1970-0400642-2openalex-snapshot
Table errata: The art of computer programming, Vol. 2: Seminumerical algorithms (Addison-Wesley, Reading, Mass., 1969) by Donald E. Knuth
inferredcites →https://doi.org/10.1093/bioinformatics/3.4.303openalex-snapshot
A computer program for the design of optimal synthetic oligonucleotide probes for protein coding genes
inferredcites →https://doi.org/10.1093/bioinformatics/4.1.19openalex-snapshot
Locating alignments with k differences for nucleotide and amino acid sequences
inferredcites →https://doi.org/10.1093/nar/10.1.197openalex-snapshot
Efficient algorithms for folding and comparing nucleic acid sequences
inferredcites →https://doi.org/10.1093/nar/14.1.501openalex-snapshot
Computer program for the IBM personal computer which searches for approximate matches to short oligonucleotide sequences in long target DNA sequences
inferredcites →https://doi.org/10.1109/fscs.1990.89530openalex-snapshot
Approximate string matching in sublinear expected time
inferredcites →https://doi.org/10.1109/sfcs.1985.22openalex-snapshot
Efficient string matching in the presence of errors
inferredcites →https://doi.org/10.1126/science.2983426openalex-snapshot
Rapid and Sensitive Protein Similarity Searches
inferredcites →https://doi.org/10.1137/0219067openalex-snapshot
An Improved Algorithm For Approximate String Matching
inferredcites →https://doi.org/10.1137/0220002openalex-snapshot
Deterministic Sampling–A New Technique for Fast Pattern Matching
inferredcites →https://doi.org/10.1145/359842.359859openalex-snapshot
A fast string searching algorithm
inferredcites →https://doi.org/10.1145/362919.362934openalex-snapshot
Implementation of the substring test by hashing
inferredcites →https://doi.org/10.1145/8307.8309openalex-snapshot
Improved string matching with k mismatches
inferredcites →https://doi.org/10.1147/rd.312.0249openalex-snapshot
Efficient randomized pattern-matching algorithms
inferredcites →https://doi.org/10.2307/2344620openalex-snapshot
An Introduction to Probability Theory and its Applications.
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/(sici)1097-024x(199612)26:12<1439::aid-spe71>3.0.co;2-1openalex-snapshot
A Comparison of Approximate String Matching Algorithms
inferred← citeshttps://doi.org/10.1007/11523468_101openalex-snapshot
Optimal Spaced Seeds for Faster Approximate String Matching
inferred← citeshttps://doi.org/10.1007/11533719_13openalex-snapshot
Rapid Homology Search with Two-Stage Extension and Daughter Seeds
inferred← citeshttps://doi.org/10.1007/3-540-45253-2_12openalex-snapshot
Range Searching over Tree Cross Products
inferred← citeshttps://doi.org/10.1007/3-540-45452-7_19openalex-snapshot
One-Gapped q-Gram Filters for Levenshtein Distance
inferred← citeshttps://doi.org/10.1007/3-540-45471-3_36openalex-snapshot
Computing the Threshold for q-Gram Filters
inferred← citeshttps://doi.org/10.1007/3-540-48194-x_6openalex-snapshot
Better Filtering with Gapped q-Grams
inferred← citeshttps://doi.org/10.1007/3-540-61258-0_4openalex-snapshot
Filtration with q-samples in approximate string matching
inferred← citeshttps://doi.org/10.1007/3-540-61680-2_69openalex-snapshot
Lempel-Ziv index for q-grams
inferred← citeshttps://doi.org/10.1007/978-1-84800-320-0openalex-snapshot
Sequence Comparison: Theory and Methods
inferred← citeshttps://doi.org/10.1007/978-3-319-59826-0_7openalex-snapshot
DNA-Seq Error Correction Based on Substring Indices
inferred← citeshttps://doi.org/10.1007/978-3-540-27801-6_22openalex-snapshot
Multi-seed Lossless Filtration
inferred← citeshttps://doi.org/10.1007/978-3-540-74126-8_32openalex-snapshot
Fast Computation of Good Multiple Spaced Seeds
inferred← citeshttps://doi.org/10.1007/978-3-540-87361-7_27openalex-snapshot
Computing Alignment Seed Sensitivity with Probabilistic Arithmetic Automata
inferred← citeshttps://doi.org/10.1007/978-3-642-00727-9_6openalex-snapshot
Amino Acid Classification and Hash Seeds for Homology Search
inferred← citeshttps://doi.org/10.1007/s00453-007-0062-yopenalex-snapshot
Rapid Homology Search with Neighbor Seeds
inferred← citeshttps://doi.org/10.1007/s11227-022-05038-6openalex-snapshot
Space-efficient computation of parallel approximate string matching
inferred← citeshttps://doi.org/10.1007/s11265-007-0087-0openalex-snapshot
Biosequence Similarity Search on the Mercury System
inferred← citeshttps://doi.org/10.1016/j.ipl.2009.07.008openalex-snapshot
Seed optimization for i.i.d. similarities is no easier than optimal Golomb ruler design
inferred← citeshttps://doi.org/10.1016/j.jcss.2003.04.002openalex-snapshot
Sensitivity analysis and efficient method for identifying optimal spaced seeds
inferred← citeshttps://doi.org/10.1016/j.jcss.2004.12.003openalex-snapshot
Designing seeds for similarity search in genomic DNA
inferred← citeshttps://doi.org/10.1016/j.jcss.2007.03.007openalex-snapshot
Optimal spaced seeds for faster approximate string matching
inferred← citeshttps://doi.org/10.1080/00207160212111openalex-snapshot
On-Line Approximate String Searching Algorithms: Survey and Experimental Results
inferred← citeshttps://doi.org/10.1089/10665270360688093openalex-snapshot
Provably Sensitive Indexing Strategies for Biosequence Similarity Search
inferred← citeshttps://doi.org/10.1089/cmb.1995.2.291openalex-snapshot
A New Algorithm for DNA Sequence Assembly
inferred← citeshttps://doi.org/10.1089/cmb.2005.12.1137openalex-snapshot
Quick, Practical Selection of Effective Seeds for Homology Search
inferred← citeshttps://doi.org/10.1089/cmb.2005.12.847openalex-snapshot
Designing Multiple Simultaneous Seeds for DNA Similarity Search
inferred← citeshttps://doi.org/10.1089/cmb.2010.0005openalex-snapshot
Error Tolerant Indexing and Alignment of Short Reads with Covering Template Families
inferred← citeshttps://doi.org/10.1093/bioinformatics/17.5.419openalex-snapshot
Efficient large-scale sequence comparison by locality-sensitive hashing
inferred← citeshttps://doi.org/10.1093/bioinformatics/17.8.676openalex-snapshot
Representation of amino acids as five-bit or three-bit patterns for filtering protein databases
inferred← citeshttps://doi.org/10.1093/bioinformatics/18.6.873openalex-snapshot
SST: an algorithm for finding near-exact sequence matches in time proportional to the logarithm of the database size
inferred← citeshttps://doi.org/10.1093/bioinformatics/btm422openalex-snapshot
Multiple spaced seeds for homology search
inferred← citeshttps://doi.org/10.1093/bioinformatics/btn416openalex-snapshot
ZOOM! Zillions of oligos mapped
inferred← citeshttps://doi.org/10.1093/bioinformatics/btp533openalex-snapshot
Updates to the RMAP short-read mapping software
inferred← citeshttps://doi.org/10.1093/bioinformatics/btq648openalex-snapshot
Anatomy of a hash-based long read sequence mapping algorithm for next generation DNA sequencing
inferred← citeshttps://doi.org/10.1093/sysbio/syw104openalex-snapshot
Homology-aware Phylogenomics at Gigabase Scales
inferred← citeshttps://doi.org/10.1101/2021.06.09.447791openalex-snapshot
VSTseed: periodic spaced seeds for reads with substitutions
inferred← citeshttps://doi.org/10.1101/gr.095190.109openalex-snapshot
High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing
inferred← citeshttps://doi.org/10.1101/gr.275648.121openalex-snapshot
Effective sequence similarity detection with strobemers
inferred← citeshttps://doi.org/10.1101/gr.277659.123openalex-snapshot
Aligning distant sequences to graphs using long seed sketches
inferred← citeshttps://doi.org/10.1109/access.2020.3031159openalex-snapshot
A Review on Sequence Alignment Algorithms for Short Reads Based on Next-Generation Sequencing
inferred← citeshttps://doi.org/10.1109/asap.2004.12openalex-snapshot
Biosequence similarity search on the Mercury system
inferred← citeshttps://doi.org/10.1109/asap.2004.1342485openalex-snapshot
Biosequence similarity search on the mercury system
inferred← citeshttps://doi.org/10.1109/bibe.2004.1317369openalex-snapshot
Estimating seed sensitivity on homogeneous alignments
inferred← citeshttps://doi.org/10.1109/dsd.2005.66openalex-snapshot
Reconfigurable Parallel Approximate String Matching on FPGAs
inferred← citeshttps://doi.org/10.1109/icips.1997.669126openalex-snapshot
A new approach to two-dimensional pattern matching allowing errors
inferred← citeshttps://doi.org/10.1109/ipdpsw.2010.5470894openalex-snapshot
pFANGS: Parallel high speed sequence mapping for Next Generation 454-roche Sequencing reads
inferred← citeshttps://doi.org/10.1109/wcre.2011.22openalex-snapshot
Approximate Code Search in Program Histories
inferred← citeshttps://doi.org/10.1128/aem.63.6.2338-2346.1997openalex-snapshot
A new computational method for detection of chimeric 16S rRNA artifacts generated by PCR amplification from mixed bacterial populations
inferred← citeshttps://doi.org/10.1142/9781848161092_0016openalex-snapshot
SEED OPTIMIZATION IS NO EASIER THAN OPTIMAL GOLOMB RULER DESIGN
inferred← citeshttps://doi.org/10.1142/s0129054108005541openalex-snapshot
INDEXING GAPPED-FACTORS USING A TREE
inferred← citeshttps://doi.org/10.1142/s0219720004000661openalex-snapshot
PATTERNHUNTER II: HIGHLY SENSITIVE AND FAST HOMOLOGY SEARCH
inferred← citeshttps://doi.org/10.1145/299432.299460openalex-snapshot
q -gram based database searching using a suffix array (QUASAR)
inferred← citeshttps://doi.org/10.1145/316542.316550openalex-snapshot
A fast bit-vector algorithm for approximate string matching based on dynamic programming
inferred← citeshttps://doi.org/10.1145/565196.565208openalex-snapshot
Provably sensitive Indexing strategies for biosequence similarity search
inferred← citeshttps://doi.org/10.1145/640075.640083openalex-snapshot
Designing seeds for similarity search in genomic DNA
inferred← citeshttps://doi.org/10.1186/1471-2105-14-69openalex-snapshot
BOND: Basic OligoNucleotide Design
inferred← citeshttps://doi.org/10.1186/1471-2105-5-149openalex-snapshot
Improved hit criteria for DNA local alignment
inferred← citeshttps://doi.org/10.1186/1471-2105-9-128openalex-snapshot
Using quality scores and longer reads improves accuracy of Solexa read mapping
inferred← citeshttps://doi.org/10.1186/1748-7188-4-3openalex-snapshot
Lossless filter for multiple repeats with bounded edit distance
inferred← citeshttps://doi.org/10.1186/s12859-023-05517-4openalex-snapshot
PerFSeeB: designing long high-weight single spaced seeds for full sensitivity alignment with a given number of mismatches
inferred← citeshttps://doi.org/10.1186/s13015-015-0062-4openalex-snapshot
HIA: a genome mapper using hybrid index-based sequence alignment
inferred← citeshttps://doi.org/10.21203/rs.3.rs-1051543/v1openalex-snapshot
PerFSeeB: Designing Long High-weight Single Spaced Seeds for Full Sensitivity Alignment with a Given Number of Mismatches
inferred← citeshttps://doi.org/10.21533/scjournal.v2i2.24openalex-snapshot
Multiple Methods for Genome Filtering
inferred← citeshttps://doi.org/10.3389/fgene.2022.1023092openalex-snapshot
A depth-first search algorithm for oligonucleotide design in gene assembly
inferred← citeshttps://doi.org/10.4028/www.scientific.net/amr.998-999.814openalex-snapshot
An Improved BMQ Algorithm for Pattern Matching
inferred← citeshttps://doi.org/10.4049/jimmunol.1700485openalex-snapshot
Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads
inferred← citeshttps://doi.org/10.48550/arxiv.0801.2378openalex-snapshot
String algorithms and data structures
inferred← citeshttps://doi.org/10.5753/isys.2018.373openalex-snapshot
Um sistema para auxiliar na seleção de regiões específicas de sequências biológicas
inferred← citeshttps://doi.org/10.6084/m9.figshare.26631232openalex-snapshot
Additional file 1 of PerFSeeB: designing long high-weight single spaced seeds for full sensitivity alignment with a given number of mismatches
inferred← citeshttps://doi.org/10.70675/61f0bd4dzc25az4991z9d80z68f70d9a3df2openalex-snapshot
Développement de méthodes et d'algorithmes pour la caractérisation et l'annotation des transcriptomes avec les séquenceurs haut débit.
inferred← citeshttps://doi.org/10.7936/k74f1nzropenalex-snapshot
Design and analysis of an accelerated seed generation stage for BLASTP on the Mercury system - Master's Thesis, August 2006
inferred← citeshttps://doi.org/10.7936/k74j0cfcopenalex-snapshot
Performance Evaluation for Hybrid Architectures
inferred← citeshttps://doi.org/10.7936/k7gq6w4nopenalex-snapshot
Design and Evaluation of a BLAST Ungapped Extension Accelerator, Master's Thesis
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