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Insertion and deletion of words: Determinism and reversibility
[chapter]
1992
Lecture Notes in Computer Science
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Necessary and sufficient conditions, under which the result of sequential insertion or deletion of two words is a singleton set, are given. ...
They are connected with the operations of sequential insertion and deletion, which are nondeterministic versions of catenation and right/ left quotient. ...
The operations of sequential insertion and sequential deletion (called in the sequel, shortly, insertion and deletion), defined and studied in [2] play an important role in understanding the mechanisms ...
doi:10.1007/3-540-55808-x_30
fatcat:qftpxik5ebfgboxuteeoifniem
SCHEMA FOR PARALLEL INSERTION AND DELETION: REVISITED
2011
International Journal of Foundations of Computer Science
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A general framework of parallel insertion and deletion based on p-schemata is proposed. A p-schema is a set of tuples of words. ...
When being used for parallel insertion of a language into a word, an element of p-schema specifies how to split the word into factors between which the language to be inserted. ...
This research was supported by Natural Sciences and Engineering Research Council of Canada Discovery Grant R2824A01, and Canada Research Chair Award to L. K. ...
doi:10.1142/s0129054111008945
fatcat:4hgm67sun5hr7j7skq3j2pb3yu
Pattern recognition of strings with substitutions, insertions, deletions and generalized transpositions
1997
Pattern Recognition
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The traditional case which has been extensively studied in the literature is the one in which Y contains substitution, insertion and deletion (SID) errors. ...
The paper includes experimental results involving sub-dictionaries of the most common English words which demonstrate the superiority of our system over existing methods. ...
Latika Khanna of the School of Computer Science at Carleton for her assistance in proofreading the manuscript. ...
doi:10.1016/s0031-3203(96)00101-x
fatcat:ptgtaxjoube2xcw2yegumqt5ze
Occurrence and Consequences of Coding Sequence Insertions and Deletions in Mammalian Genomes
2004
Genome Research
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Overall, we found an excess of deletions over insertions, particularly for the rat lineage (70% excess). Sequence slippage accounts for at least 52% of insertions and 38% of deletions. ...
There is a specific enrichment of CpG dinucleotides in close proximity to insertion events, and both insertions and deletions are more common in higher G+C content sequences. ...
M.S.T. and R.R.C. are supported by the Wellcome Trust and C.P.P. by the UK Medical Research Council. The publication costs of this article were defrayed in part by payment of page charges. ...
doi:10.1101/gr.1977804
pmid:15059996
pmcid:PMC383299
fatcat:uxma372gwrfrpf5accjh7zpyg4
Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes
2003
Nucleic Acids Research
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Nucleotide substitution, insertion and deletion (indel) events are the major driving forces that have shaped genomes. ...
However, unexpectedly, the frequency of 3 bp deletions (in contrast to 3 bp insertions) violates this trend, being considerably higher than that of 2 bp deletions. ...
ACKNOWLEDGEMENTS Z.Z. thanks Paul Harrison for scintillating discussions and Duncan Milburn, Yin Liu and Nat Echols for computational assistance. ...
doi:10.1093/nar/gkg745
pmid:12954770
pmcid:PMC203328
fatcat:4peybwjfwbhongr2m2ue2wg2o4
Efficient human paternity testing with a panel of 40 short insertion-deletion polymorphisms
2010
Genetics and Molecular Research
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Thus, especially because of its simplicity and low cost, and the fact that it is composed of genomic markers that have very low mutation rates, it represents a useful new tool for human paternity testing ...
The average heterozygosity (gene diversity) per locus was 0.48, and the combined probability of identity (matching probability) for the 40-locus set was 3.48 x 10 -17 . ...
ACKNOWLEDGMENTS Research supported by CNPq of Brazil. J.R. Pimenta was the recipient of a fellowship from the Rhae Program of CNPq. ...
doi:10.4238/vol9-1gmr838
pmid:20391344
fatcat:4ohffkjl3vhqrfjf75arfnl6du
Multiple homoplasious insertions and deletions of a Triticeae (Poaceae) DNA transposon: a phylogenetic perspective
2007
BMC Evolutionary Biology
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Conclusion: Combined, the phylogenetic distribution, sequence variation, and Entrez database comparisons indicate that a Stowaway-like element has undergone multiple deletions from and insertions into ...
The high MITE copy number in grass genomes suggests an active history of amplification and insertion, but ongoing MITE activity has only rarely been seen, and ongoing Stowaway activity has never been observed ...
Acknowledgements Thanks to members of the Wichman Lab transposable element journal club (Holly Wichman, LuAnn Scott, Mac Cantrell, and Issac Erickson) and to Brandon Gaut for valuable comments on an earlier ...
doi:10.1186/1471-2148-7-92
pmid:17570855
pmcid:PMC1925063
fatcat:meo3soyplvg5vkg45opdrmsqlu
Linear Time Additively Exact Algorithm for Transformation of Chain-Cycle Graphs for Arbitrary Costs of Deletions and Insertions
2020
Mathematics
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We assume that the double cut and join operations have identical costs, and costs of the deletion and insertion operations are arbitrary strictly positive rational numbers. ...
We propose a novel linear time algorithm which, given any directed weighted graphs a and b with vertex degrees 1 or 2, constructs a sequence of operations transforming a into b. ...
Acknowledgments: We are grateful to the anonymous reviewers for their thorough review, and we highly appreciate the comments and suggestions, which significantly contributed to improving the quality of ...
doi:10.3390/math8112001
fatcat:5zdo5di3tbgatnp3qlozvg3krq
RNA-Editing with Combined Insertion and Deletion Preserves Regularity
2013
Scientific Annals of Computer Science
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The formalism here allows for simultaneous insertion and deletion of string elements. ...
We consider two elementary forms of string rewriting called guided insertion/deletion and guided rewriting. ...
Acknowledgements We acknowledge fruitful feedback from Peter van der Gulik and detailed comment from the reviewers. ...
doi:10.7561/sacs.2013.1.39
fatcat:tbjfvn4eofepfb6drg77aihc5m
On the embedding capacity of DNA strands under substitution, insertion, and deletion mutations
2010
Media Forensics and Security II
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On the embedding capacity of DNA strands under substitution, insertion, and deletion mutations Felix Balado, Proc. SPIE 7541, 754114 (2010). http://dx.doi.org/ ...
This is the main topic studied in this paper, where we consider that DNA sequences may be subject to substitution, insertion, and deletion mutations. ...
We will consider herein three important types of mutations: substitutions, insertions and deletions. ...
doi:10.1117/12.838537
dblp:conf/mediaforensics/Balado10
fatcat:2rtupx6pxra5pokxcckefqjvey
Correlated Occurrence and Bypass of Frame-Shifting Insertion-Deletions (InDels) to Give Functional Proteins
2013
PLoS Genetics
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Short insertions and deletions (InDels) comprise an important part of the natural mutational repertoire. InDels are, however, highly deleterious, primarily because two-thirds result in frame-shifts. ...
Besides an expected 8A repeat, other types of repeats, including short ones, and G and C repeats, were bypassed. ...
Summary Homonucleotide repeats are exceptionally prone to insertions and/or deletions of bases (InDels). ...
doi:10.1371/journal.pgen.1003882
pmid:24204297
pmcid:PMC3812077
fatcat:25nretm7drector5s5ayrmbfle
List decoding subspace codes from insertions and deletions
2012
Proceedings of the 3rd Innovations in Theoretical Computer Science Conference on - ITCS '12
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We present a construction of subspace codes along with an efficient algorithm for list decoding from both insertions and deletions, handling an information-theoretically maximum fraction of these with ...
Ours is the first list decoding algorithm for subspace codes that can handle deletions; even one deletion can totally distort the structure of the basis of a subspace and is thus challenging to handle. ...
(The ratios t/ℓ and r/ℓ are the fraction of insertions and deletions, respectively.) Proof. ...
doi:10.1145/2090236.2090252
dblp:conf/innovations/GuruswamiNW12
fatcat:jntjs2l5s5aefoolcvyolol2ea
Identification and Characterization of a Cryptic Genomic Deletion-Insertion in EYA1 Associated with Branchio-Otic Syndrome
2021
Neural Plasticity
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Sanger sequencing of this PCR product revealed that it is in fact a GRCh38/hg38:chr8:g.71318554_71374171delinsTGCC genomic deletion-insertion. ...
Real-time PCR at multiple regions of EYA1 confirmed the existence of this genomic deletion and extended its 5 ′ boundary beyond the 5 ′ -UTR. ...
The Government of China is also acknowledged for providing research grant. ...
doi:10.1155/2021/5524381
pmid:33880118
pmcid:PMC8046558
fatcat:3kop7awaonavlgzn6ymv6d5634
Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part IV: Incorporation of substitutions and other mutations
[article]
2015
bioRxiv
pre-print
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via insertions and deletions along time axis. ...
BackgroundInsertions and deletions (indels) account for more nucleotide differences between two related DNA sequences than substitutions do, and thus it is imperative to develop a stochastic evolutionary ...
In other words, F (x, δ ′ ω [l]) inserts δ ′ ω [l] between the x th and (x +1) th residues of ω ∈ Ω L( s ) . ...
doi:10.1101/023622
fatcat:omnq5uz7ubfwnacqrlszyisali
Deletion and duplication of the adenomatous polyposis coli gene resulting from an interchromosomal insertion involving 5(q22q23.3) in the father
2000
Journal of Medical Genetics
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The authors would like to thank Simon Roth who referred the proband to the Cytogenetics Department and Helwyn Morgan for referring subsequent prenatal samples. ...
Interchromosomal insertions are individually rare events and in this family both a deletion and duplication of the inserted region were viable. ...
In other words, alleles of genes whose products interfere with the determination, migration, or diVerentiation of ganglion cells of the enteric plexuses might, in the presence of a perturbed Ras signalling ...
doi:10.1136/jmg.37.2.141
pmid:10712105
pmcid:PMC1734530
fatcat:3uxp4up72rdsjfsfn7uoea2dwy
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