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Covering Codes using Insertions or Deletions [article]

Andreas Lenz, Cyrus Rashtchian, Paul H. Siegel, Eitan Yaakobi
2020 arXiv   pre-print
Finally, we derive improved upper bounds for covering codes using R≥ 2 insertions or deletions.  ...  While most prior work on covering codes has focused on the Hamming metric, we consider the problem of designing covering codes defined in terms of either insertions or deletions.  ...  about covering codes using insertions or deletions.  ... 
arXiv:1911.09944v4 fatcat:7p7gixn3cre2nb7xrhbn6b5d2m

Incremental compilation of optimized code

Lori L. Pollock, Mary Lou Soffa
1985 Proceedings of the 12th ACM SIGACT-SIGPLAN symposium on Principles of programming languages - POPL '85  
Changes to the optimized code which either destroy optimizations or create conditions for further optimizations are incorporated into the model and the optimized code without recompiling unaffected optimizations  ...  Techniques to incrementally compile locally optimized code, given intermediate code modifications are developed using a program representation based on flow graphs and dags.  ...  Deletion of a store (redefinition) to one of the operands (A or B) of a common subexpression. Deletion of a store to, or use of, the variable defined in the later common subexpression (D).  ... 
doi:10.1145/318593.318629 dblp:conf/popl/PollockS85 fatcat:g56arcq5gvc6la25jkqh2pmnba

Algorithms for the Maximum Hamming Distance Problem [chapter]

Ola Angelsmark, Johan Thapper
2005 Lecture Notes in Computer Science  
We then give small covering codes that use either a single deletion or a single insertion, or -in one algorithm -two deletions.  ...  Discovering covering codes for edit distance is important in its own right, since very little work is known.  ...  However, with edit distance, we can cover strings by using insertions, deletions, or a combination of these.  ... 
doi:10.1007/11402763_10 fatcat:f4torhyuyzg6rjs5k5fblc2mw4

RacketLogger: Logging and Visualising Changes in DrRacket

Turgut Reis Kursun, Jens Van der Plas, Quentin Stiévenart, Coen De Roover
2022 Zenodo  
Developers frequently make code changes while programming, such as deleting a line of code and renaming or introducing a variable.  ...  The logged changes, in both forms, are useful because they can be used to build new software engineering tools, such as static code analysers.  ...  on what nodes have been updated, inserted, deleted, or have remained unchanged.  ... 
doi:10.5281/zenodo.6326893 fatcat:eap7vi3c5fgi5jwhisgaulr3ka

Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants

Aziz Belkadi, Alexandre Bolze, Yuval Itan, Aurélie Cobat, Quentin B. Vincent, Alexander Antipenko, Lei Shang, Bertrand Boisson, Jean-Laurent Casanova, Laurent Abel
2015 Proceedings of the National Academy of Sciences of the United States of America  
In the regions targeted by WES capture (81.5% of the consensus coding genome), the mean numbers of single-nucleotide variants (SNVs) and small insertions/deletions (indels) detected per sample were 84,192  ...  The estimated mean number of real coding SNVs (656 variants, ∼3% of all coding HQ SNVs) identified by WGS and missed by WES was greater than the number of SNVs identified by WES and missed by WGS (26 variants  ...  Finally, we investigated in more detail the coding regions and corresponding genes that were either poorly covered or not covered at all by the WES kit we used.  ... 
doi:10.1073/pnas.1418631112 pmid:25827230 pmcid:PMC4418901 fatcat:ey2sbh5pmzduzdegdu35rvlb6m

Efficient instrumentation for code coverage testing

Mustafa M. Tikir, Jeffrey K. Hollingsworth
2002 Software engineering notes  
The traditional approach for code coverage tools is to use static code instrumentation.  ...  In this paper we present a new approach to dynamically insert and remove instrumentation code to reduce the runtime overhead of code coverage.  ...  instrumentation code can be deleted or not.  ... 
doi:10.1145/566185.566186 fatcat:kkch7ej23jahnbthejxzzpl6l4

Guest Editorial Special Issue: "From Deletion-Correction to Graph Reconstruction: In Memory of Vladimir I. Levenshtein"

Alexander Barg, Lara Dolecek, Ryan Gabrys, Gyula O. H. Katona, János Körner, Andrew McGregor, Olgica Milenkovic, Sihem Mesnager, Gilles Zémor
2021 IEEE Transactions on Information Theory  
The article "Covering codes using insertions or deletions," by Lenz et al., considers the problem of designing covering codes under the Levenshtein distance.  ...  The Levenshtein distance equals the smallest number of insertions, deletions, or substitutions required to convert one string into another.  ... 
doi:10.1109/tit.2021.3072555 dblp:journals/tit/BargDGKKMMMZ21 fatcat:ebzt3z72yjfwtbiqczqjqzwzk4

Efficient instrumentation for code coverage testing

Mustafa M. Tikir, Jeffrey K. Hollingsworth
2002 Software engineering notes  
The traditional approach for code coverage tools is to use static code instrumentation.  ...  In this paper we present a new approach to dynamically insert and remove instrumentation code to reduce the runtime overhead of code coverage.  ...  instrumentation code can be deleted or not.  ... 
doi:10.1145/566172.566186 dblp:conf/issta/TikirH02 fatcat:5seweskimzab5bignavyugejy4

Efficient instrumentation for code coverage testing

Mustafa M. Tikir, Jeffrey K. Hollingsworth
2002 Software engineering notes  
The traditional approach for code coverage tools is to use static code instrumentation.  ...  In this paper we present a new approach to dynamically insert and remove instrumentation code to reduce the runtime overhead of code coverage.  ...  instrumentation code can be deleted or not.  ... 
doi:10.1145/566171.566186 fatcat:f5yzchlau5egvmo3hrnrdiqmsu

Multiversion Linear Quadtree for Spatio-Temporal Data [chapter]

Theodoros Tzouramanis, Michael Vassilakopoulos, Yannis Manolopoulos
2001 Lecture Notes in Computer Science  
We also conducted a thorough experimentation using sequences of real and synthetic raster images.  ...  Thus, the new structure may be used as an index mechanism for storing and accessing evolving raster images.  ...  Bernhard Seeger of the University of Marburg for kindly providing the MVBT code.  ... 
doi:10.1007/3-540-44472-6_22 fatcat:7oirpvfoinfqhdjmw4jyu2p5qi

DNA indels in coding regions reveal selective constraints on protein evolution in the human lineage

Nicole de la Chaux, Philipp W Messer, Peter F Arndt
2007 BMC Evolutionary Biology  
Here we focus on recent DNA insertions and deletions in protein coding regions of the human genome to investigate selective constraints on indels in protein evolution.  ...  Amino acid insertion and deletion rates in genes associated with elementary biochemical reactions (e. g. catalytic activity, ligase activity, electron transport, or catabolic process) are lower compared  ...  DNA indels in coding sequence lead to insertions or deletions of amino acids in the translated proteins.  ... 
doi:10.1186/1471-2148-7-191 pmid:17935613 pmcid:PMC2151769 fatcat:jrapgk6ccfddjgackwpbzc24pu

A Parallel Implementation for Determining Genomic Distances Under Deletion and Insertion [chapter]

Vijaya Smitha Kolli, Hui Liu, Michelle Hong Pan, Yi Pan
2005 Lecture Notes in Computer Science  
They are especially interested in the scenarios in which the genome evolves through insertions, deletions, and movements of genes along its chromosomes.  ...  Marron et al proposed a polynomial-time approximation algorithm to compute (near) minimum edit distances under inversions, deletions, and unrestricted insertions.  ...  into another, where insertion, deletion and inversion are the process of adding, deleting and reversing a single or sequence of genes in the existing gene sequence respectively.  ... 
doi:10.1007/11428848_127 fatcat:j4nxj54x55fuvglevypbpvdf6u

Genetic diagnosis of Duchenne/Becker muscular dystrophy using next-generation sequencing: validation analysis of DMD mutations

Mariko Okubo, Narihiro Minami, Kanako Goto, Yuichi Goto, Satoru Noguchi, Satomi Mitsuhashi, Ichizo Nishino
2016 Journal of Human Genetics  
We designed a multiplex primer pool for DMD and sequenced 67 cases having different mutations: 37 with deletions/ duplications and 30 with small mutations or short insertions/deletions in DMD, using an  ...  The results were compared with those from MLPA or Sanger sequencing. All deletions were detected. In contrast, 50% of duplications were correctly identified compared with the MLPA method.  ...  We used multiplex primer pools covering 100% of the coding region, comprising 161 amplicons for 79 exons. One to four amplicons covered each exon except exon 79, which was covered by 13 amplicons.  ... 
doi:10.1038/jhg.2016.7 pmid:26911353 pmcid:PMC4931045 fatcat:p3o54tc2f5girbydzogkdvd2qy

Genetic diagnosis of Duchenne/Becker muscular dystrophy using next-generation sequencing: Validation analysis of DMD mutations

M. Okubo, N. Minami, K. Goto, S. Noguchi, S. Mitsuhashi, I. Nishino
2016 Neuromuscular Disorders  
We designed a multiplex primer pool for DMD and sequenced 67 cases having different mutations: 37 with deletions/ duplications and 30 with small mutations or short insertions/deletions in DMD, using an  ...  The results were compared with those from MLPA or Sanger sequencing. All deletions were detected. In contrast, 50% of duplications were correctly identified compared with the MLPA method.  ...  We used multiplex primer pools covering 100% of the coding region, comprising 161 amplicons for 79 exons. One to four amplicons covered each exon except exon 79, which was covered by 13 amplicons.  ... 
doi:10.1016/j.nmd.2016.06.041 fatcat:asxihxbi65hxnpj4u7cklzaana

Nomenclature for the description of human sequence variations

J. den Dunnen, S. Antonarakis
2001 Human Genetics  
However, current rules do not yet cover all types of mutations, nor do they cover more complex mutations.  ...  ., the DNA level, using either a genomic or a cDNA reference sequence.  ...  However, current rules do not yet cover all types of mutations, nor do they cover more complex mutations.  ... 
doi:10.1007/s004390100505 pmid:11479744 fatcat:2bq7vr6hbjdgxjkzljjz5no5he
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