Tag: Liftoff

October 2023: 1,000 wheat exome SNP data as a track on the IWGSC Chinese Spring RefSeq v2.1 genome browser

1,000 wheat exome SNP data were created as a track on the IWGSC Chinese Spring RefSeq v2.1 genome browser based on the Vasudevan and Cloutier, BMC Research Notes, 2023. Press here to see the track on the IWGSC Chinese Spring RefSeq v2.1 genome browser. Excerpts from the abstract:The 1,000 wheat…

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Op-ed | Space Force launch strategy a step in the right direction

The Space Force next year will select launch providers for Phase 3 of the National Security Space Launch (NSSL) program. Industry proposals are due Dec. 15. This next phase of NSSL marks a significant evolution in how the Space Force approaches launch, leaning into the commercial market in a way…

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Genomic signatures of convergent shifts to plunge-diving behavior in birds

Wyles, J. S., Kunkel, J. G. & Wilson, A. C. Birds, behavior, and anatomical evolution. Proc. Natl Acad. Sci. 80, 4394–4397 (1983). Article  CAS  PubMed  PubMed Central  Google Scholar  Lapiedra, O., Sol, D., Carranza, S. & Beaulieu, J. M. Behavioural changes and the adaptive diversification of pigeons and doves. Proc….

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Lifting of the 1,000 wheat exome project SNPs from Triticum aestivum cv. Chinese Spring assembly RefSeq v1.0 to RefSeq v2.1

Abstract Objective The 1,000 wheat exome project captured the single nucleotide variants in the coding regions of a diverse set of 890 wheat accessions to analyse the contribution of introgression to adaptation of wheat. However, this highly useful single nucleotide polymorphism (SNP) dataset is based on RefSeq v1.0 of the…

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Assembly of 43 human Y chromosomes reveals extensive complexity and variation

Skaletsky, H. et al. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423, 825–837 (2003). Article  ADS  CAS  PubMed  Google Scholar  Porubsky, D. et al. Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders. Cell 185, 1986–2005 (2022). Article …

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Investigating open reading frames in known and novel transcripts using ORFanage

O’Leary, N. A. et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion and functional annotation. Nucleic Acids Res. 44, D733–D745 (2016). Google Scholar  Frankish, A. et al. GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Res. 51, D942–D949 (2023). Google Scholar  Pertea,…

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reference annotation for the human and mouse genomes in 2023

D942–D949 Nucleic Acids Research, 2023, Vol. 51, Database issue Published online 24 November 2022 doi.org/10.1093/nar/gkac1071 GENCODE: reference annotation for the human and mouse genomes in 2023 Adam Frankish 1,* , Sı́lvia Carbonell-Sala2 , Mark Diekhans 3 , Irwin Jungreis 4,5 , Jane E. Loveland 1 , Jonathan M. Mudge1 ,…

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A pangenome reference of 36 Chinese populations

Populations and samples For Phase I of the CPC project, we selected 68 samples from 731 individuals with genomes deep-sequenced using next-generation sequencing. Following a previous study5, we applied a procedure to quantitatively evaluate the genetic diversity coverage based on principal component analysis results. We selected individuals using a statistic…

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Allen Institute takes on a supporting role in experiment to grow stem cells in space

A live colony of human induced pluripotent stem cells fills the screen of a microscope. (Allen Institute Photo) Space: The final frontier … for stem cells? Seattle’s Allen Institute for Cell Science says cells from its collection are going into space for the first time on a private mission to…

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Repeat masking for genome annotation

Repeat masking for genome annotation 0 I am working on a (plant) genome annotation pipeline and would like some advice regarding repeat masking. My pipeline consists of running several ab-initio gene prediction tools (Augustus, GlimmerHMM and SNAP) + transcript alignment (PASA) + protein alignment (genomeThreader) evidence + gene liftover (liftoff),…

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Annelid functional genomics reveal the origins of bilaterian life cycles

Hall, B. K. & Wake, M. H. in The Origin and Evolution of Larval Forms (eds Hall, B. K. & Wake, M. H.) 1–19 (Academic Press, 1999). Nielsen, C. Animal phylogeny in the light of the trochaea theory. Biol. J. Linn. Soc. 25, 243–299 (2008). Article  Google Scholar  Garstang, W….

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Researchers Grow Stem Cells Aboard International Space Station In New Study

Scientists are growing stem cells in space in an effort to discover new ways to produce large batches of certain stem cells to treat a variety of diseases. Researchers from Cedars-Sinai Medical Center in Los Angeles are behind the program that delivered stem cells to the International Space Station (ISS)…

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wont recognize the gtf or gff3 files (runtime exception)

snpeff : wont recognize the gtf or gff3 files (runtime exception) 1 Hi, I am trying to build a custom databasee for snpeff. As instructed both in the forum and snpeff instructions, I did the following; Then I added the following into snpEff.config file # BG94_1 BG94_1.genome : BG94_1 Then…

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Are there any alternatives to Liftoff

Are there any alternatives to Liftoff – Mapping annotations (GFF/GTF) between assemblies 2 Hi, I am annotating closely related accession (varieties) using reference assembly (please note that I am using only a region, so that is the reason why you don’t see chromosome info). I really liked liftoff (ver 1.6.1:…

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Blank output When converting GFF3 file to GTF using either gffread or AGAT

Blank output When converting GFF3 file to GTF using either gffread or AGAT 1 Hi, I am trying to convert gff3 file (please see below) to GTF. I used two tools suggested here gffread and agat here. #gff-version 3 Bg_94-1_CX35|chr01_10700000_16500000 Liftoff gene 1 1345 . + . ID=gene_1;Name=Os01g0293800 gene;coverage=0.997;sequence_ID=0.982;extra_copy_number=0;copy_num_ID=gene_1_0 Bg_94-1_CX35|chr01_10700000_16500000…

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local variable ‘feature_db’ referenced before assignment

Hi, I want to map annotations from rich gencode human gtf or gff3 to great apes’ genome. I tried to run liftoff (github.com/agshumate/Liftoff) but it returns error the below. Following the github issue’s post, I confirmed there’s no _db file before running, the annotation file is .gff3, the permission of…

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