Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases

Priyam, Anurag; Woodcroft, Ben J.; Rai, Vivek; Moghul, Ismail; Munagala, Alekhya; Ter, Filip; Chowdhary, Hiten; Pieniak, Iwo Lukasz; Maynard, Lawrence J; Gibbins, Mark Anthony; Moon, HongKee; Davis-Richardson, Austin G.; Uludağ, Mahmut; Watson-Haigh, Nathan S.; Challis, Richard; Nakamura, Hiroyuki; Favreau, Emeline; Gómez, Esteban A.; Pluskal, Tomáš; Leonard, Guy; Rumpf, Wolfgang; Wurm, Yannick

doi:10.1093/molbev/msz185

Cited by 173 publications

(96 citation statements)

References 13 publications

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“…Our curation pipeline is described in detail in Supporting Information Methods. Briefly, we iteratively performed blastn and blastp (Camacho et al ; Priyam et al ) searches of the fire ant genome assembly (Wurm et al. ) using as queries the previously known fire ant OBP sequences as well as UniProt sequences that are part of the Pfam family “PBP_GOBP” (Finn et al ; UniProt Consortium ).…”

Section: Methodsmentioning

confidence: 99%

Fire ant social chromosomes: Differences in number, sequence and expression of odorant binding proteins

et al. 2017

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Section: Methodsmentioning

confidence: 99%

Fire ant social chromosomes: Differences in number, sequence and expression of odorant binding proteins

et al. 2017

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“…Figure shows the data for the circadian gene Es‐period as it is found on the website, including functional information. As an extra resource, the peptide assembly, coding assembly, and total assembly are available as searchable BLAST databases using the SequenceServer front end (Priyam et al., ), permitting fast, simple identification of genes of interest.…”

Section: Resultsmentioning

confidence: 99%

The Euphausia superba transcriptome database, SuperbaSE: An online, open resource for researchers

Hunt

Özkaya

Davies

et al. 2017

Ecology and Evolution

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Antarctic krill (Euphausia superba) is a crucial component of the Southern Ocean ecosystem, acting as the major link between primary production and higher trophic levels with an annual predator demand of up to 470 million tonnes. It also acts as an ecosystem engineer, affecting carbon sequestration and recycling iron and nitrogen, and has increasing importance as a commercial product in the aquaculture and health industries. Here we describe the creation of a de novo assembled head transcriptome for E. superba. As an example of its potential as a molecular resource, we relate its exploitation in identifying and characterizing numerous genes related to the circadian clock in E. superba, including the major components of the central feedback loop. We have made the transcriptome openly accessible for a wider audience of ecologists, molecular biologists, evolutionary geneticists, and others in a user‐friendly format at SuperbaSE, hosted at http://www.krill.le.ac.uk.

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“…Several genes that are only expressed during early embryo development can now be found in the reference transcriptome, such as Oct3/4, Nanog, Oobox and H1foo. The updated assembly has been uploaded to a permanent data repository (https://doi.org/10.5281/zenodo.1188364) and is accessible via our BLAST search website: http://spinymouse.erc.monash.edu/sequenceserver/ ("Trinity_v2.3.2_plus_embryo-specific_transcripts") (Priyam et al, 2015). This approach significantly improved gene-level resolution and improved the reference transcriptome for future applications.…”

Section: Discussionmentioning

confidence: 99%

Embryonic gene transcription in the spiny mouse (Acomys cahirinus): an investigtion into the embryonic genome activation

Mamrot

Temple-Smith

Dickinson

2018

Preprint

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Our understanding of genetic mechanisms driving early embryonic development is primarily based on experiments conducted on mice, however translation of findings can be limited by physiological differences between mice and humans. To address this, we investigated whether the spiny mouse (Acomys cahirinus) is a closer model of early human embryonic development due to their more human-like endocrine profile. We therefore characterised the initiation of gene transcription in the spiny mouse embryo and compared the pattern of gene expression during the embryonic genome activation (EGA) with common mouse and human embryos. Naturally-mated spiny mouse embryos were obtained at the 2-cell, 4-cell and 8-cell stages of development (n=4 biological replicates per stage). RNA-Seq of these samples produced 709.1M paired-end reads in total. De novo assembly of reads was conducted using Trinity. Embryo-specific transcripts were extracted from the de novo assembly and added to the reference spiny mouse transcriptome . Transcription was first detected between the 2cell and 4-cell stages for the majority of genes (n=3,428), with fewer genes first transcribed between the 4-cell and 8-cell stages (n=1,150). The pattern of gene expression in spiny mouse embryos during this period of development is more human-like than common mouse embryos. This is the first evidence the spiny mouse may provide a more suitable model of human embryonic development. The improved reference Acomys cahirinus transcriptome is publically accessible, further increasing the value of this tool for ongoing research. Further investigation into early development in the spiny mouse is warranted.

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Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases

Cited by 173 publications

References 13 publications

Fire ant social chromosomes: Differences in number, sequence and expression of odorant binding proteins

Fire ant social chromosomes: Differences in number, sequence and expression of odorant binding proteins

The Euphausia superba transcriptome database, SuperbaSE: An online, open resource for researchers

Embryonic gene transcription in the spiny mouse (Acomys cahirinus): an investigtion into the embryonic genome activation

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