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genBlastG: using BLAST searches to build homologous gene models

Rong She, Jeffrey Shih-Chieh Chu, Bora Uyar, Jun Wang, Ke Wang, Nansheng Chen
2011 Computer applications in the biosciences : CABIOS  
Results: Here we report an efficient algorithm, genBlastG that directly uses the HSPs reported by BLAST to define high-quality gene models.  ...  Motivation: BLAST users frequently expect to obtain homologous genes with certain similarity to their query genes.  ...  These issues are not considered in genBlastA. genBlastG builds gene models by maximizing the similarity to their corresponding queries.  ... 
doi:10.1093/bioinformatics/btr342 pmid:21653517 fatcat:7s57tvzufvew3hl4kemnorj3qu

New techniques and tools in 2011

Elaine Ellerton, Harald Hutter
2012 Worm  
She et al. took advantage of the speed of BLAST and used the local alignments produced by BLAST as input for an algorithm (genBlastG) to build gene models by exploiting sequence signals to identify introns  ...  do not necessarily identify homologous genes.  ... 
doi:10.4161/worm.19575 pmid:24058819 pmcid:PMC3670167 fatcat:ccs3bh7pn5ejfmq3l7dmwtyfui

WormBase

Kevin Howe, Paul Davis, Michael Paulini, Mary Ann Tuli, Gary Williams, Karen Yook, Richard Durbin, Paul Kersey, Paul W. Sternberg
2012 Worm  
We also review our approaches to sequence curation, and discuss the impact on annotation quality of large functional genomics projects such as modENCODE.  ...  Gene predictions by genBlastG 49 based on BLAST homologies to C. elegans proteins have also proved valuable for the curation of C. briggsae, C. brenneri, and C. remenei.  ...  These can be used both to confirm introns already part of curated gene models, and also to suggest changes to existing gene models or new isoforms.  ... 
doi:10.4161/worm.19574 pmid:24058818 pmcid:PMC3670165 fatcat:2q474cfv7vg3lbzszuzizdocsm

Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features

Hiroaki Iwata, Osamu Gotoh
2012 Nucleic Acids Research  
Spliced alignment plays a central role in the precise identification of eukaryotic gene structures.  ...  The datasets are designed to correspond to various real situations, i.e. divergent eukaryotic species, different types of reference sequences, and the wide divergence between query and target sequences  ...  ACKNOWLEDGEMENTS We would like to thank Dr D. Lu for providing the test data and the detailed results of the Pairagon project. We also thank Drs T. Yada, N. Ichinose and M.  ... 
doi:10.1093/nar/gks708 pmid:22848105 pmcid:PMC3488211 fatcat:wgidpmavxfctrm2bdjtzbhhhge

The Bear Giant-Skipper genome suggests genetic adaptations to living inside yucca roots

Qian Cong, Wenlin Li, Dominika Borek, Zbyszek Otwinowski, Nick V. Grishin
2018 Molecular Genetics and Genomics  
Their lower heterozygosity helped us to obtain a high-quality genome with an N50 of 4.2 Mbp. The ~ 430 Mb genome encodes about 14000 proteins.  ...  Giant-Skippers are attributed to the subfamily Hesperiinae and they are endemic to southern and mostly desert regions of the North American continent.  ...  All applicable international, national, and institutional guidelines for the care and use of animals were followed.  ... 
doi:10.1007/s00438-018-1494-6 pmid:30293092 pmcid:PMC6436644 fatcat:jg52iylypfgznbrxgp7wugns64

The genome sequence of the soft-rot fungus Penicillium purpurogenum reveals a high gene dosage for lignocellulolytic enzymes

Wladimir Mardones, Alex Di Genova, María Paz Cortés, Dante Travisany, Alejandro Maass, Jaime Eyzaguirre
2018 Mycology  
RNA-seq was performed and 93.1% of the reads aligned to the assembled genome.  ...  These results demonstrate the great potential for lignocellulolytic activity of this fungus and the possible use of its enzymes in related industrial applications.  ...  This set of sequences was used to perform a Blast search against P. purpurogenum genes.  ... 
doi:10.1080/21501203.2017.1419995 pmid:30123662 pmcid:PMC6059080 fatcat:5fxbniyucbhvplyzoz52fifi3m

Tiger Swallowtail Genome Reveals Mechanisms for Speciation and Caterpillar Chemical Defense

Qian Cong, Dominika Borek, Zbyszek Otwinowski, Nick V. Grishin
2015 Cell Reports  
We obtained the genome from a wild-caught specimen using a cost-effective strategy that overcomes the high (2%) heterozygosity problem.  ...  Comparative genomics of appropriate model organisms holds the promise of making it possible. However, the high heterozygosity of many Eukaryotes currently prohibits assembling their genomes.  ...  This work was supported in part by the NIH (GM094575 to N.V.G.) and the Welch Foundation (I-1505 to N.V.G.).  ... 
doi:10.1016/j.celrep.2015.01.026 pmid:25683714 pmcid:PMC8935626 fatcat:aguktihjgvgkvm3ji4w7hr2rxi

The genome of Onchocerca volvulus, agent of river blindness

James A. Cotton, Sasisekhar Bennuru, Alexandra Grote, Bhavana Harsha, Alan Tracey, Robin Beech, Stephen R. Doyle, Matthew Dunn, Julie C. Dunning Hotopp, Nancy Holroyd, Taisei Kikuchi, Olivia Lambert (+15 others)
2016 Nature Microbiology  
Further species-specific gene models were provided to MAKER using comparative algorithms against the genome: genBlastG (ref. 78 ) output of C. elegans gene models (WormBase 79 ) and RATT (Rapid Annotation  ...  Subsequently, the predicted wOv proteins were used to search for regions with protein homology in the O. volvulus genome using TBLASTN as implemented in NCBI Table 16 ).  ... 
doi:10.1038/nmicrobiol.2016.216 pmid:27869790 pmcid:PMC5310847 fatcat:64gyzdb37bh2dlr25rjhb4iblq

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

R. E. Green, E. L. Braun, J. Armstrong, D. Earl, N. Nguyen, G. Hickey, M. W. Vandewege, J. A. St. John, S. Capella-Gutierrez, T. A. Castoe, C. Kern, M. K. Fujita (+43 others)
2014 Science  
In brief, sequence searches were used to retrieve homologs (E-value 10 -5 , 50% overlap) in a set of vertebrates (17) .  ...  The evolutionary model best fitting the data was used to build an ML tree with PhyML (68) using four rate categories and a fraction of invariable sites, estimated from the data.  ... 
doi:10.1126/science.1254449 pmid:25504731 pmcid:PMC4386873 fatcat:mb3cuxtsfzeutptxgbdcycpg4e

The genome sequence of the soft-rot fungus Penicillium purpurogenum reveals a high gene dosage for lignocellulolytic enzymes [article]

Jaime Eyzaguirre, Wladimir Mardones, Alex Di Genova, Maria Paz Cortes, Dante Travisany, Alejandro Maass
2017 bioRxiv   pre-print
P. purpurogenum shows a higher number of proteins with CAZy motifs, transcription factors and transporters as compared to other sequenced Penicillia.  ...  These results demonstrate the great potential for lignocellulolytic activity of this fungus and the possible use of its enzymes in related industrial applications.  ...  This set of sequences was used to perform a 242 Blast search against P. purpurogenum genes. was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity  ... 
doi:10.1101/197368 fatcat:v3fjytkqoja5jkuvypts4el4aa

An introgressed gene causes meiotic drive in Neurospora sitophila [article]

Jesper Svedberg, Aaron A. Vogan, Nicholas A. Rhoades, Dilini Sarmarajeewa, David J. Jacobson, Martin Lascoux, Thomas M Hammond, Hanna Johannesson
2020 bioRxiv   pre-print
In this study, we identify the gene responsible for spore killing in Sk-1 by generating both long and short-read genomic data and by using these data to perform a genome wide association test.  ...  Spk-1 is not related to other known meiotic drive genes, and similar sequences are only found within Neurospora.  ...  -C., Uyar, B., Wang, J., Wang, K., and Chen, N. (2011). genBlastG: using BLAST 832 searches to build homologous gene models.  ... 
doi:10.1101/2020.01.29.923946 fatcat:xl4mvozfa5au3jdoniuv6fldby

A coffee berry borer (Hypothenemus hampei) genome assembly reveals a reduced chemosensory receptor gene repertoire and male-specific genome sequences

Lucio Navarro-Escalante, Erick M Hernandez-Hernandez, Jonathan Nuñez, Flor E Acevedo, Alejandro Berrio, Luis M Constantino, Beatriz E Padilla-Hurtado, Diana Molina, Carmenza Gongora, Ricardo Acuña, Jeff Stuart, Pablo Benavides
2021 Scientific Reports  
Using genome and transcriptome data, we annotated the genes associated with chemosensation and found a reduced gene repertoire composed by 67 odorant receptors (ORs), 62 gustatory receptors (GRs), 33 ionotropic  ...  In silico transcript abundance analysis of these chemosensory genes revealed expression enrichment in CBB adults compared with larva.  ...  as references for homology-based sequence finding with genBlastG (She et al., 2011) against the CBB genome scaffolds and TBLASTN search against the transcriptome sequences.  ... 
doi:10.1038/s41598-021-84068-1 pmid:33649370 pmcid:PMC7921381 fatcat:di5wppcrbbawpkcokyesrdiy4q

Genome-wide signatures of convergent evolution in echolocating mammals

Joe Parker, Georgia Tsagkogeorga, James A. Cotton, Yuan Liu, Paolo Provero, Elia Stupka, Stephen J. Rossiter
2013 Nature  
Processing and analyses of sequence data was undertaken by G.T., with input from E.S., who also conducted gene ontology analyses with P.P.  ...  Mein (Barts and the London Genome Centre) for providing access to computing facilities, and for assistance with running analyses. We are also grateful to S. Dodsworth, R. Buggs, K. Davies, J.  ...  This was achieved by performing reciprocal blast searches against a database consisting of the gene models for the four bats, and using as queries the human sequences of 11,185 genes reported as 1-to-1  ... 
doi:10.1038/nature12511 pmid:24005325 pmcid:PMC3836225 fatcat:h6cpzjrsx5crliecakgos66tou

Comparative genomics of the major parasitic worms

2018 Nature Genetics  
We have identified gene family births and hundreds of expanded gene families at key nodes in the phylogeny that are relevant to parasitism.  ...  Examples include gene families that modulate host immune responses, enable parasite migration though host tissues or allow the parasite to feed.  ...  All have been submitted to GenBank under the BioProject IDs listed in Supplementary Table 1.  ... 
doi:10.1038/s41588-018-0262-1 pmid:30397333 pmcid:PMC6349046 fatcat:ksx7pyge2vc2pjsaoktseodwym

The whale shark genome reveals patterns of vertebrate gene family evolution

Milton Tan, Anthony K Redmond, Helen Dooley, Ryo Nozu, Keiichi Sato, Shigehiro Kuraku, Sergey Koren, Adam M Phillippy, Alistair DM Dove, Timothy Read
2021 eLife  
Finally, we found gene families that shifted in expansion rate in vertebrate giants were enriched for human cancer-related genes, consistent with gigantism requiring adaptations to suppress cancer.  ...  We found chondrichthyan and giant vertebrate genomes had decreased substitution rates compared to other vertebrates, but gene family expansion rates varied among vertebrate giants, suggesting substitution  ...  were performed using BLAST+ 752 v2.6.0 to identify putative homologs of TLRs, NLRs and RLRs (Altschul et al., 1990).  ... 
doi:10.7554/elife.65394 pmid:34409936 pmcid:PMC8455134 fatcat:teuhgkwkkrfifokrfxcxooxwyq
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