FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W4200042858> ?p ?o ?g. }

• W4200042858 abstract "Millions of species are currently being sequenced, and their genomes are being compared. Many of them have more complex genomes than model systems and raise novel challenges for genome alignment. Widely used local alignment strategies often produce limited or incongruous results when applied to genomes with dispersed repeats, long indels, and highly diverse sequences. Moreover, alignment using many-to-many or reciprocal best hit approaches conflicts with well-studied patterns between species with different rounds of whole-genome duplication. Here, we introduce Anchored Wavefront alignment (AnchorWave), which performs whole-genome duplication-informed collinear anchor identification between genomes and performs base pair-resolved global alignment for collinear blocks using a two-piece affine gap cost strategy. This strategy enables AnchorWave to precisely identify multikilobase indels generated by transposable element (TE) presence/absence variants (PAVs). When aligning two maize genomes, AnchorWave successfully recalled 87% of previously reported TE PAVs. By contrast, other genome alignment tools showed low power for TE PAV recall. AnchorWave precisely aligns up to three times more of the genome as position matches or indels than the closest competitive approach when comparing diverse genomes. Moreover, AnchorWave recalls transcription factor-binding sites at a rate of 1.05- to 74.85-fold higher than other tools with significantly lower false-positive alignments. AnchorWave complements available genome alignment tools by showing obvious improvement when applied to genomes with dispersed repeats, active TEs, high sequence diversity, and whole-genome duplication variation." @default.
• W4200042858 created "2021-12-31" @default.
• W4200042858 creator A5020150778 @default.
• W4200042858 creator A5041038026 @default.
• W4200042858 creator A5043258949 @default.
• W4200042858 creator A5052502603 @default.
• W4200042858 creator A5055879350 @default.
• W4200042858 creator A5088729105 @default.
• W4200042858 date "2021-12-21" @default.
• W4200042858 modified "2023-10-14" @default.
• W4200042858 title "AnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication" @default.
• W4200042858 cites W1981239255 @default.
• W4200042858 cites W1994145712 @default.
• W4200042858 cites W2012986985 @default.
• W4200042858 cites W2021044098 @default.
• W4200042858 cites W2055043387 @default.
• W4200042858 cites W2057857382 @default.
• W4200042858 cites W2076658876 @default.
• W4200042858 cites W2082703775 @default.
• W4200042858 cites W2093931624 @default.
• W4200042858 cites W2094923272 @default.
• W4200042858 cites W2106208020 @default.
• W4200042858 cites W2106389870 @default.
• W4200042858 cites W2106678197 @default.
• W4200042858 cites W2108234281 @default.
• W4200042858 cites W2110284618 @default.
• W4200042858 cites W2128489434 @default.
• W4200042858 cites W2138098955 @default.
• W4200042858 cites W2144857133 @default.
• W4200042858 cites W2150654633 @default.
• W4200042858 cites W2162758337 @default.
• W4200042858 cites W2163471569 @default.
• W4200042858 cites W2166469005 @default.
• W4200042858 cites W2170806459 @default.
• W4200042858 cites W2184041281 @default.
• W4200042858 cites W2401562190 @default.
• W4200042858 cites W2477297434 @default.
• W4200042858 cites W2623168030 @default.
• W4200042858 cites W2737673717 @default.
• W4200042858 cites W2784788330 @default.
• W4200042858 cites W2789843538 @default.
• W4200042858 cites W2802282671 @default.
• W4200042858 cites W2884730312 @default.
• W4200042858 cites W2898245710 @default.
• W4200042858 cites W2905453209 @default.
• W4200042858 cites W2912355480 @default.
• W4200042858 cites W2952105401 @default.
• W4200042858 cites W2953169567 @default.
• W4200042858 cites W2955598626 @default.
• W4200042858 cites W2964820234 @default.
• W4200042858 cites W2982979721 @default.
• W4200042858 cites W2987444591 @default.
• W4200042858 cites W2992029569 @default.
• W4200042858 cites W3012600779 @default.
• W4200042858 cites W3027536938 @default.
• W4200042858 cites W3086678357 @default.
• W4200042858 cites W3092370645 @default.
• W4200042858 cites W3125142766 @default.
• W4200042858 cites W3162278365 @default.
• W4200042858 cites W3164610320 @default.
• W4200042858 cites W3166805469 @default.
• W4200042858 cites W3189525949 @default.
• W4200042858 cites W3193218983 @default.
• W4200042858 cites W3205442753 @default.
• W4200042858 cites W4200042858 @default.
• W4200042858 doi "https://doi.org/10.1073/pnas.2113075119" @default.
• W4200042858 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/34934012" @default.
• W4200042858 hasPublicationYear "2021" @default.
• W4200042858 type Work @default.
• W4200042858 citedByCount "21" @default.
• W4200042858 countsByYear W42000428582021 @default.
• W4200042858 countsByYear W42000428582022 @default.
• W4200042858 countsByYear W42000428582023 @default.
• W4200042858 crossrefType "journal-article" @default.
• W4200042858 hasAuthorship W4200042858A5020150778 @default.
• W4200042858 hasAuthorship W4200042858A5041038026 @default.
• W4200042858 hasAuthorship W4200042858A5043258949 @default.
• W4200042858 hasAuthorship W4200042858A5052502603 @default.
• W4200042858 hasAuthorship W4200042858A5055879350 @default.
• W4200042858 hasAuthorship W4200042858A5088729105 @default.
• W4200042858 hasBestOaLocation W42000428581 @default.
• W4200042858 hasConcept C104317684 @default.
• W4200042858 hasConcept C105176652 @default.
• W4200042858 hasConcept C119054055 @default.
• W4200042858 hasConcept C135763542 @default.
• W4200042858 hasConcept C141231307 @default.
• W4200042858 hasConcept C151020129 @default.
• W4200042858 hasConcept C153209595 @default.
• W4200042858 hasConcept C174600577 @default.
• W4200042858 hasConcept C189206191 @default.
• W4200042858 hasConcept C2910714999 @default.
• W4200042858 hasConcept C3742359 @default.
• W4200042858 hasConcept C4918238 @default.
• W4200042858 hasConcept C54355233 @default.
• W4200042858 hasConcept C70721500 @default.
• W4200042858 hasConcept C7602840 @default.
• W4200042858 hasConcept C78458016 @default.
• W4200042858 hasConcept C86803240 @default.
• W4200042858 hasConceptScore W4200042858C104317684 @default.
• W4200042858 hasConceptScore W4200042858C105176652 @default.

• next