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Companion: a web server for annotation and analysis of parasite genomes

Sascha Steinbiss, Fatima Silva-Franco, Brian Brunk, Bernardo Foth, Christiane Hertz-Fowler, Matthew Berriman, Thomas D. Otto
2016 Nucleic Acids Research  
To overcome those needs we have developed the Companion web server (http://companion. sanger.ac.uk) providing parasite genome annotation as a service using a reference-based approach.  ...  We demonstrate the use and performance of Companion by annotating two Leishmania and Plasmodium genomes as typical parasite cases and evaluate the results compared to manually annotated references.  ...  ACKNOWLEDGEMENTS The authors would like to thank Stephen Beverley and Wesley Warren for providing a diverse set of kinetoplastid genomes for testing the pipeline, Peter Myler and Gowthaman Ramasamy for  ... 
doi:10.1093/nar/gkw292 pmid:27105845 pmcid:PMC4987884 fatcat:p4oulubu4zcltnnaipaaedk52u

Molecular Methods for Detection of Antimicrobial Resistance [chapter]

Muna F. Anjum, Ea Zankari, Henrik Hasman
2018 Antimicrobial Resistance in Bacteria from Livestock and Companion Animals  
The strengths and weaknesses of these methods are discussed, especially in the context of implementing them for routine surveillance activities on a global scale for mitigating the risk posed by AMR worldwide  ...  Based on current popularity and ease of use, PCR and single-isolate whole-genome sequencing seem irreplaceable.  ...  KmerResistance KmerResistance (73) is a mapping tool and is available both as a web server and as a command-line tool.  ... 
doi:10.1128/9781555819804.ch3 fatcat:tzqnwltsbbhhdesffe25r7e2bq

Complete and de novo assembly of the Leishmania braziliensis (M2904) genome

Sandra González-de la Fuente, Esther Camacho, Ramón Peiró-Pastor, Alberto Rastrojo, Fernando Carrasco-Ramiro, Begoña Aguado, Jose M Requena
2018 Memórias do Instituto Oswaldo Cruz  
The public availability of this information will contribute to a better knowledge of this pathogen and help in the search for vaccines and novel drug targets aimed to control the disease caused by this  ...  Here, we report the assembly of the L. braziliensis (M2904) genome into 35 continuous chromosomes. Also, the annotation of 8395 genes is provided.  ...  (25) Gene annotation of both protein-coding genes and known non-coding RNAs on the new assembled L. braziliensis genome was performed using Companion web server, using the default settings and selecting  ... 
doi:10.1590/0074-02760180438 pmid:30540030 pmcid:PMC6319030 fatcat:23u5fy647va5nevvwa3ensux3a

LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis

Felipe Torres, Raúl Arias-Carrasco, José C. Caris-Maldonado, Aldina Barral, Vinicius Maracaja-Coutinho, Artur T. L. De Queiroz
2017 Database: The Journal of Biological Databases and Curation  
These poorly annotated coding genes and ncRNAs could be important players for the understanding of this protozoan biology, the mechanisms behind host-parasite interactions and disease control.  ...  This updated information can be useful for future genomics, transcriptomics and metabolomics studies; being an additional tool for genome annotation pipelines and novel studies associated with the understanding  ...  Ricardo Khouri and Dr. Rubens Monte-Neto for the helpful discussions during the development of LeishDB and the preparation of this manuscript.  ... 
doi:10.1093/database/bax047 pmid:29220437 pmcid:PMC5502370 fatcat:5nvrydnrkngezneltah6r7rj3m

Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes

T. Wylie
2004 Nucleic Acids Research  
Nematode.net (www.nematode.net) is a web accessible resource for investigating gene sequences from nematode genomes.  ...  Nematodes also parasitize livestock and companion animals and cause over 80 billion dollars in crop damage annually ( 2 , 3 ).  ...  Both NemaGene clusters and individual ESTs can be searched for sequence identity using the online NemaBLAST tool, which utilizes a local WUBLAST server ( 12) (http://blast.wustl.edu).  ... 
doi:10.1093/nar/gkh010 pmid:14681448 pmcid:PMC308745 fatcat:alqmlkbvfng3zm36kcgfknephu

Real time, field-deployable whole genome sequencing of malaria parasites using nanopore technology [article]

Zahra Razook, Somya Mehra, Brittany Gilchhrist, Digjaya Utama, Dulcie Lautu-Gumal, Abebe Fola, Didier Menard, James Kazura, Moses Laman, Ivo Mueller, Leanne Robinson, Melanie Bahlo (+1 others)
2020 bioRxiv   pre-print
Nanopore sequencing will expedite genomic surveillance of malaria and provide new insights into parasite genome biology.  ...  Malaria parasite genomes have been generated predominantly using short read sequencing technology which can be slow, requires advanced laboratory training and does not adequately interrogate complex genomic  ...  Thank you also to Celine Barnadas for facilitating access to Cambodian samples and Stuart Lee for assistance with genomic analyses.  ... 
doi:10.1101/2020.12.17.423341 fatcat:fnbh56vscvalrl2rwloe6hfcyu

Complete assembly of the Leishmania donovani (HU3 strain) genome and transcriptome annotation

Esther Camacho, Sandra González-de la Fuente, Alberto Rastrojo, Ramón Peiró-Pastor, Jose Carlos Solana, Laura Tabera, Francisco Gamarro, Fernando Carrasco-Ramiro, Jose M. Requena, Begoña Aguado
2019 Scientific Reports  
Leishmania donovani is a unicellular parasite that causes visceral leishmaniasis, a fatal disease in humans. In this study, a complete assembly of the genome of L. donovani is provided.  ...  Alternative SL addition sites and heterogeneity in the poly-A addition sites were commonly observed for most of the genes.  ...  Acknowledgements We are extremely grateful to all the support, advice and help received by our colleagues from the Genomics and Next Generation Sequencing Core Facility at the CBMSO.  ... 
doi:10.1038/s41598-019-42511-4 pmid:30992521 pmcid:PMC6467909 fatcat:lrxrj5bk5nafdeteknmbu7sfuq

Resequencing of the Leishmania infantum (strain JPCM5) genome and de novo assembly into 36 contigs

Sandra González-de la Fuente, Ramón Peiró-Pastor, Alberto Rastrojo, Javier Moreno, Fernando Carrasco-Ramiro, Jose M. Requena, Begoña Aguado
2017 Scientific Reports  
Leishmania parasites are the causative of leishmaniasis, a group of potentially fatal human diseases. Control strategies for leishmaniasis can be enhanced by genome based investigations.  ...  The complete annotation of the new genome (GFF3 file) is provided in the Supplementary file 1 in Excel format. Synteny analysis.  ...  Acknowledgements The authors appreciate the advice and helpful comments received from members of the Genomics and Next Generation Sequencing Service at the CBMSO.  ... 
doi:10.1038/s41598-017-18374-y pmid:29273719 pmcid:PMC5741766 fatcat:x3f5n2vcxjbd5llj2v7i635a7u

Gene Annotation and Transcriptome Delineation on a De Novo Genome Assembly for the Reference Leishmania major Friedlin Strain

Esther Camacho, Sandra González-de la Fuente, Jose C. Solana, Alberto Rastrojo, Fernando Carrasco-Ramiro, Jose M. Requena, Begoña Aguado
2021 Genes  
The Friedlin strain of this species (LmjF) was chosen when a multi-laboratory consortium undertook the objective of deciphering the first genome sequence for a parasite of the genus Leishmania.  ...  Here, we present a new assembly for the genome of this strain (named LMJFC for clarity), generated by the combination of two high throughput sequencing platforms, Illumina short-read sequencing and PacBio  ...  Acknowledgments: We thank the Genomics and NGS Core Facility at the Centro de Biología Molecular Severo Ochoa (CBMSO, CSIC-UAM) for helping with the bioinformatics analysis.  ... 
doi:10.3390/genes12091359 pmid:34573340 pmcid:PMC8468144 fatcat:yvpkp35w2fdxfkbdtrxrdqxr7q

PacBio assembly of a Plasmodium knowlesi genome sequence with Hi-C correction and manual annotation of the SICAvar gene family

S. A. LAPP, J. A. GERALDO, J.-T. CHIEN, F. AY, S. B. PAKALA, G. BATUGEDARA, J. HUMPHREY, J. D. DeBARRY, K. G. Le ROCH, M. R. GALINSKI, J. C. KISSINGER
2017 Parasitology  
This sequence and annotation, referred to as the 'MaHPIC Pk genome sequence', includes manual annotation of the SICAvar gene family with 136 full-length members categorized as type I or II.  ...  SUMMARY Plasmodium knowlesi has risen in importance as a zoonotic parasite that has been causing regular episodes of malaria throughout South East Asia.  ...  Second, the assembled genome sequence was submitted to the Companion Web server (Steinbiss et al. 2016) for annotation and analysis of parasite genomes using a reference-based approach.  ... 
doi:10.1017/s0031182017001329 pmid:28720171 pmcid:PMC5798397 fatcat:oe6smag7pbbrhc44nvae4odpbi

Genome Analysis of Endotrypanum and Porcisia spp., Closest Phylogenetic Relatives of Leishmania, Highlights the Role of Amastins in Shaping Pathogenicity

Amanda T. S. Albanaz, Evgeny S. Gerasimov, Jeffrey J. Shaw, Jovana Sádlová, Julius Lukeš, Petr Volf, Fred R. Opperdoes, Alexei Y. Kostygov, Anzhelika Butenko, Vyacheslav Yurchenko
2021 Genes  
Most significantly, the analysis of gene family evolution revealed a substantially reduced repertoire of surface proteins, such as amastins and biopterin transporters BT1 in the Endotrypanum/Porcisia species  ...  This reduction was especially pronounced for δ-amastins, a subfamily of cell surface proteins crucial in the propagation of Leishmania amastigotes inside vertebrate macrophages and, apparently, dispensable  ...  Acknowledgments: We thank members of our laboratories for stimulating discussions. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/genes12030444 pmid:33804709 fatcat:jjbmcoheonbi3enmupigpjoco4

Carbohydrate-Active Enzymes in Pythium and Their Role in Plant Cell Wall and Storage Polysaccharide Degradation

Marcelo M. Zerillo, Bishwo N. Adhikari, John P. Hamilton, C. Robin Buell, C. André Lévesque, Ned Tisserat, Olivier Lespinet
2013 PLoS ONE  
var. sporangiiferum and Py. vexans) using the "CAZymes Analysis Toolkit" and "Database for Automated Carbohydrate-active Enzyme Annotation" and compared them to previously published oomycete genomes.  ...  lack the requisite genes for the complete saccharification of these carbohydrates for use as a carbon source.  ...  Acknowledgments We want to thank Lindsay Triplett for the assistance in the phylogenetic analysis and Jorge Ibarra Caballero for the support in bioinformatics.  ... 
doi:10.1371/journal.pone.0072572 pmid:24069150 pmcid:PMC3772060 fatcat:7z26ahkpajalnn3t3bcq3c6v7u

Genomic and transcriptomic evidence for descent from Plasmodium and loss of blood schizogony in Hepatocystis parasites from naturally infected red colobus monkeys

Eerik Aunin, Ulrike Böhme, Theo Sanderson, Noah D. Simons, Tony L. Goldberg, Nelson Ting, Colin A. Chapman, Chris I. Newbold, Matthew Berriman, Adam J. Reid, Tim J.C. Anderson
2020 PLoS Pathogens  
We show transcriptomic support for a lack of replication in the blood and genomic support for a complete loss of a family of genes involved in red blood cell invasion.  ...  Hepatocystis is a genus of single-celled parasites infecting, amongst other hosts, monkeys, bats and squirrels.  ...  Acknowledgments We would like to thank Alan Tracey for advice on genome assembly and J. Byaruhanga, P. Katurama, A. Mbabazi, A. Nyamwija, J. Rusoke, D. Hyeroba and G.  ... 
doi:10.1371/journal.ppat.1008717 pmid:32745123 fatcat:o5tclydwzzajthwybo63i7w6sa

The UCSC Archaeal Genome Browser: 2012 update

P. P. Chan, A. D. Holmes, A. M. Smith, D. Tran, T. M. Lowe
2011 Nucleic Acids Research  
The UCSC Archaeal Genome Browser (http:// archaea.ucsc.edu) offers a graphical web-based resource for exploration and discovery within archaeal and other selected microbial genomes.  ...  By bringing together existing gene annotations, gene expression data, multiple-genome alignments, pre-computed sequence comparisons and other specialized analysis tracks, the genome browser is a powerful  ...  We thank Kira Makarova, Yuri Wolf and the arCOGs team in Evolutionary Genomics Research Group of NCBI for support and input in the development of the arCOGs Browser.  ... 
doi:10.1093/nar/gkr990 pmid:22080555 pmcid:PMC3245099 fatcat:nbatgfqcjbfqbbwg7a5alvbcyq

Genomic and transcriptomic evidence for descent from Plasmodium and loss of blood schizogony in Hepatocystis parasites from naturally infected red colobus monkeys [article]

Eerik Aunin, Ulrike Boehme, Theo Sanderson, Noah D Simons, Tony L Goldberg, Nelson Ting, Colin A Chapman, Chris I Newbold, Matthew Berriman, Adam James Reid
2019 bioRxiv   pre-print
We show transcriptomic support for a lack of replication in the blood and genomic support for a complete loss of a family of genes involved in red blood cell invasion.  ...  Hepatocystis is a genus of single-celled parasites infecting monkeys, bats and squirrels.  ...  Acknowledgements We would like to thank Alan Tracey for advice on genome assembly and J. Byaruhanga, P.  ... 
doi:10.1101/871327 fatcat:lg4dpreggvcg7ou2bxjpbhsdsu
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