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De novo identification of highly diverged protein repeats by probabilistic consistency

A. Biegert, J. Söding
2008 Computer applications in the biosciences : CABIOS  
Results: We present HHrepID, a method for the de novo identification of repeats in protein sequences.  ...  Motivation: An estimated 25% of all eukaryotic proteins contain repeats, which underlines the importance of duplication for evolving new protein functions.  ...  Financial support by the Max-Planck-Society and partial support by the Center for Integrated Protein Science Munich (CIPSM) is gratefully acknowledged. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btn039 pmid:18245125 fatcat:kk6yipkoerb7fm2r2b2setoeai

Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution

Biao Wang, Robert Ekblom, Ignas Bunikis, Heli Siitari, Jacob Höglund
2014 BMC Genomics  
However, de novo sequencing of the whole genome of an organism remains non-trivial.  ...  Results: We generated 133 Gbp of sequence data from one black grouse individual by the SOLiD platform and used a combination of de novo assembly and chicken reference genome mapping to assemble the reads  ...  The sequencing was performed by the Uppsala Sequencing Centre and the SNIC-UPPMAX high-performance computing cluster was utilized for computations.  ... 
doi:10.1186/1471-2164-15-180 pmid:24602261 pmcid:PMC4022176 fatcat:57gx27pc3jh67igfztuayidkia

Two Low Coverage Bird Genomes and a Comparison of Reference-Guided versus De Novo Genome Assemblies

Daren C. Card, Drew R. Schield, Jacobo Reyes-Velasco, Matthew K. Fujita, Audra L. Andrew, Sara J. Oyler-McCance, Jennifer A. Fike, Diana F. Tomback, Robert P. Ruggiero, Todd A. Castoe, Sergios-Orestis Kolokotronis
2014 PLoS ONE  
We used these data to estimate de novo genome assemblies and referenceguided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation  ...  Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo  ...  Disclaimer: Any use of trade, product, or firm names in this publication is for descriptive purposes only and does not imply endorsement by the U.S. Government. Author Contributions  ... 
doi:10.1371/journal.pone.0106649 pmid:25192061 pmcid:PMC4156343 fatcat:omlbhht2avdtpf7tmpdxdxrrlm

PepExplorer: A Similarity-driven Tool for Analyzingde NovoSequencing Results

Felipe V. Leprevost, Richard H. Valente, Diogo B. Lima, Jonas Perales, Rafael Melani, John R. Yates, Valmir C. Barbosa, Magno Junqueira, Paulo C. Carvalho
2014 Molecular & Cellular Proteomics  
PepExplorer can read the output of various widely adopted de novo sequencing tools and converge to a list of proteins with a global false-discovery rate.  ...  With this as motivation, PepExplorer was developed to use rigorous pattern recognition to assemble a list of homologue proteins using de novo sequencing data coupled to sequence alignment to allow biological  ...  of protein identification through statistical mapping of de novo sequencing results to a protein sequence database.  ... 
doi:10.1074/mcp.m113.037002 pmid:24878498 pmcid:PMC4159663 fatcat:z2gbz5czlbcktou6h2ot4pfufe

A draft genome sequence of the elusive giant squid, Architeuthis dux

Rute R da Fonseca, Alvarina Couto, Andre M Machado, Brona Brejova, Carolin B Albertin, Filipe Silva, Paul Gardner, Tobias Baril, Alex Hayward, Alexandre Campos, Ângela M Ribeiro, Inigo Barrio-Hernandez (+32 others)
2020 GigaScience  
We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome.  ...  size of 2.7 Gb, and a scaffold N50 of 4.8 Mb.  ...  Hestbjerg Hansen for help with generating sequencing data; Shawn Hoon for sharing transcriptome data; Annie Lingren for help with sample shipping; and Peter Smith for providing samples and the support of  ... 
doi:10.1093/gigascience/giz152 pmid:31942620 pmcid:PMC6962438 fatcat:xe3j657275eg5jisgdwwhcv4sq

A high-quality genome assembly for the endangered golden snub-nosed monkey (Rhinopithecus roxellana)

Lu Wang, Jinwei Wu, Xiaomei Liu, Dandan Di, Yuhong Liang, Yifei Feng, Suyun Zhang, Baoguo Li, Xiao-Guang Qi
2019 GigaScience  
In the new genome, 22,497 protein-coding genes were predicted, of which 22,053 were functionally annotated.  ...  Thus, important information such as genome structural variation and repeat sequences may be absent.  ...  Jiang Chang from the Discipline Development Department of Northwest University for their support. This study was supported through the Discipline Construction Project of Northwest University.  ... 
doi:10.1093/gigascience/giz098 pmid:31437279 pmcid:PMC6705546 fatcat:ekttlttxuzajddllcmsxhk33qq

Software Evaluation for de novo Detection of Transposons [article]

Matias Rodriguez, Wojciech Makalowski
2021 biorxiv/medrxiv   pre-print
However, despite their relevance the identification of TEs is not an easy task and a number of tools were developed to tackle this problem.  ...  To better understand how they perform, we tested several widely used tools for de novo TE detection and compared their performance on both simulated data and well curated genomic sequences.  ...  obtained by the TE de novo!  ... 
doi:10.1101/2021.02.08.430290 fatcat:ami77uelevcohi4xoplkxgjpi4

A call for benchmarking transposable element annotation methods

Douglas R. Hoen, Glenn Hickey, Guillaume Bourque, Josep Casacuberta, Richard Cordaux, Cédric Feschotte, Anna-Sophie Fiston-Lavier, Aurélie Hua-Van, Robert Hubley, Aurélie Kapusta, Emmanuelle Lerat, Florian Maumus (+6 others)
2015 Mobile DNA  
This lack of accuracy assessment calls into question conclusions from a wide range of research that depends explicitly or implicitly on TE annotation.  ...  DNA derived from transposable elements (TEs) constitutes large parts of the genomes of complex eukaryotes, with major impacts not only on genomic research but also on how organisms evolve and function.  ...  Acknowledgements This work was funded by a Bioinformatics and Computational Biology grant to MB and TB from Genome Canada, Genome Québec, and the Canadian Institutes for Health Research.  ... 
doi:10.1186/s13100-015-0044-6 pmid:26244060 pmcid:PMC4524446 fatcat:g6rnuade2nc4ljrnkqlpt66v5y

A beginner's guide to manual curation of transposable elements

Clement Goubert, Rory J. Craig, Agustin F. Bilat, Valentina Peona, Aaron A. Vogan, Anna V. Protasio
2022 Mobile DNA  
Results Our manuscript attempts to fill this gap by providing a set of detailed computer protocols, software recommendations and video tutorials for those aiming to manually curate TEs.  ...  Detailed step-by-step protocols, aimed at the complete beginner, are presented in the Supplementary Methods.  ...  We would like to emphasise that the tools presented here are just a few of the many excellent tools available for sequence analysis, some of them developed with TE annotation in mind, others repurposed  ... 
doi:10.1186/s13100-021-00259-7 pmid:35354491 pmcid:PMC8969392 fatcat:6bkxngp6yvbr7p46qwvfrhbeke

A network-based comparative framework to study conservation and divergence of proteomes in plant phylogenies

Junha Shin, Harald Marx, Alicia Richards, Dries Vaneechoutte, Dhileepkumar Jayaraman, Junko Maeda, Sanhita Chakraborty, Michael Sussman, Klaas Vandepoele, Jean-Michel Ané, Joshua Coon, Sushmita Roy
2020 Nucleic Acids Research  
Module-level comparative analysis of groups of proteins shows that proteins that are more highly expressed tend to be more conserved.  ...  Globally we find that protein levels diverge according to phylogenetic distance but is more constrained than the mRNA level.  ...  using two strategies: rule-based approach and de novo clustering.  ... 
doi:10.1093/nar/gkaa1041 pmid:33219668 fatcat:kbpt6mu4mna5tftdqmin4ltfse

Genomic insights into salt adaptation in a desert poplar

Tao Ma, Junyi Wang, Gongke Zhou, Zhen Yue, Quanjun Hu, Yan Chen, Bingbing Liu, Qiang Qiu, Zhuo Wang, Jian Zhang, Kun Wang, Dechun Jiang (+30 others)
2013 Nature Communications  
Despite the high economic and ecological importance of forests, our knowledge of the genomic evolution of trees under salt stress remains very limited.  ...  Its genome is very similar and collinear to that of the closely related mesophytic congener, P. trichocarpa.  ...  Identification of PSGs.  ... 
doi:10.1038/ncomms3797 pmid:24256998 fatcat:3g2s5a3xwvabjcybw65v5zpxwa

The Basics of Protein Sequence Analysis [chapter]

Katarzyna H. Kaminska, Kaja Milanowska, Janusz M. Bujnicki
2008 Prediction of Protein Structures, Functions, and Interactions  
JMB has worked on this article while being supported by the Institute of Medical Science at the University of Tokyo.  ...  KHK has worked on this article while being supported by a fellowship from EMBO and a travel grant from Polish Academy of Sciences and JSPS.  ...  / De novo motif finder.  ... 
doi:10.1002/9780470741894.ch1 fatcat:5mafpeqhyjadlme2dmsl7weymq

Computational Identification of Novel Genes: Current and Future Perspectives

Steffen Klasberg, Tristan Bitard-Feildel, Ludovic Mallet
2016 Bioinformatics and Biology Insights  
Some of these novel genes were proposed to have evolved de novo, ie, out of noncoding sequences, whereas some have been shown to follow a duplication and divergence process.  ...  Identification of novel genes remains however a challenging task.  ...  An important subset of novel genes are grouped under the term de novo. 23 De novo genes are characterized by their mechanism of origin, which consists of their creation out of previously noncoding sequences  ... 
doi:10.4137/bbi.s39950 pmid:27493475 pmcid:PMC4970615 fatcat:6rbtbdxmf5hz5nthw6hgesrl3m

Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato [article]

Nicola Nadeau, Mayte Ruiz, Patricio Salazar, Brian Counterman, Jose Alejandro Medina, Humberto Ortiz-Zuazaga, Anna Morrison, W. Owen McMillan, Chri Jiggins, Riccardo Papa
2013 biorxiv/medrxiv   pre-print
We compare two approaches for analysis of this type of data; alignment to a reference genome and de novo assembly, and find that alignment gives the best results for species both closely (H. melpomene)  ...  Hybrid zones between subspecies of Heliconius butterflies can be very narrow and are maintained by strong selection acting on colour pattern.  ...  Santiago Villamar ın from the Museo Ecuatoriano de Ciencias Naturales provided institutional support in Ecuador.  ... 
doi:10.1101/000208 fatcat:pt5ytphjqbe3hepbx7bloxjvhm

Population genomics of parallel hybrid zones in the mimetic butterflies,H. melpomeneandH. erato

Nicola J. Nadeau, Mayté Ruiz, Patricio Salazar, Brian Counterman, Jose Alejandro Medina, Humberto Ortiz-Zuazaga, Anna Morrison, W. Owen McMillan, Chris D. Jiggins, Riccardo Papa
2014 Genome Research  
We compare two approaches for analysis of this type of data-alignment to a reference genome and de novo assembly-and find that alignment gives the best results for species both closely (H. melpomene) and  ...  Hybrid zones between subspecies of Heliconius butterflies can be very narrow and are maintained by strong selection acting on color pattern.  ...  Santiago Villamar ın from the Museo Ecuatoriano de Ciencias Naturales provided institutional support in Ecuador.  ... 
doi:10.1101/gr.169292.113 pmid:24823669 pmcid:PMC4120085 fatcat:572k53pcyndbbpzcsnzdz26ati
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