VectorBase: a home for invertebrate vectors of human pathogens

Lawson, Daniel; Arensburger, Peter; Atkinson, Peter W.; Besansky, Nora J.; Bruggner, Robert V.; Butler, Ryan; Campbell, Kathryn S.; Christophides, George K.; Christley, Scott; Dialynas, Emmanuel; Emmert, David B.; Hammond, Martin; Hill, Catherine A.; Kennedy, Ryan; Lobo, Neil F.; MacCallum, Robert M.; Madey, Gregory R.; Mégy, Karyn; Redmond, Seth; Russo, Susan M.; Severson, David W.; Stinson, Eric O.; Topalis, Pantelis; Zdobnov, Evgeni M.; Birney, Ewan; Gelbart, William M.; Kafatos, Fotis C.; Louis, Christos; Collins, Frank H.

doi:10.1093/nar/gkl960

Cited by 112 publications

(95 citation statements)

References 13 publications

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“…Recently, an increasing amount of initiatives for global data recording have been proposed to manage clinical and molecular information about infectious diseases (epiPATH, Amadoz and Gonzales-candelas, 2007), but also to focus on either human pathogenic bacteria (e.g. pathoMIPer, Thiyagarajan et al, 2006;pyloriBASE, Ahmed et al 2007; VectorBase, Lawson et al, 2007;DengueInfo, Schreiber et al, 2007) or on plant pathogens (e.g. PhiBASE, Winnenburg et al, 2006).…”

Section: -3 Universality Of the Barcode Of Life Data System (Bold)mentioning

confidence: 99%

Four years of DNA barcoding: Current advances and prospects

Frézal

Leblois

2008

Infection, Genetics and Evolution

297

202

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Section: -3 Universality Of the Barcode Of Life Data System (Bold)mentioning

confidence: 99%

Four years of DNA barcoding: Current advances and prospects

Frézal

Leblois

2008

Infection, Genetics and Evolution

297

202

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“…To identify homologs in the Ixodes scapularis Say genome, the FASTA3 software version 3.4 (Pearson and Lipman, 1988) was used to perform a local BLASTX scan of supercontig downloads from vector base (Lawson et al, 2007) (http://iscapularis.vectorbase.org/ GetData/Downloads) using the deduced AamOatp as query. To identify coding exons, the retrieved I. scapularis supercontigs were scanned against Drosophila sequences using BLASTX analysis.…”

Section: Identification Of Aamoatp Homologs In Ixodes Scapularis Genomementioning

confidence: 99%

Molecular and biological characterization of the Amblyomma americanum organic anion transporter polypeptide

Mulenga

Khumthong

Chalaire

et al. 2008

Journal of Experimental Biology

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SUMMARYThe organic anion transporting polypeptides (Oatps in rodents and other organism; OATPs in human) are Na + -independent transporters that shuttle a wide range of endogenous and xenobotic amphipathic compounds across plasma membranes. We previously discovered an Amblyomma americanum tick (Aam) Oatp cDNA among genes that were upregulated or induced in ticks that were stimulated to start feeding. In this study, we have characterized a 2860 bp full-length cDNA that encode a 724 amino acid putative protein. Bioinformatics and hydropathy analyses revealed that, in addition to the kazal-type serine proteinase inhibitor motif, AamOatp possess typical features that characterize the Oatp/OATP protein family, including 12 transmembrane (TM) domains, the consensus amino acid motif D-X-RW-(I,V)-GAWW-X-G-(F,L)-L and 11 consensus cysteine residues in the large extracellular domain between TM9 and TM10. AamOatp is constitutively and ubiquitously expressed, as determined by RT-PCR amplification of the transcript, in all organs of ticks that fed for 1-7 days. Analysis of the normalized transcript abundance revealed that from days 1 to 5 of feeding, AamOatp mRNA expression in the midgut (MG) was 60-80-fold higher than levels found in the salivary gland (SG), ovary (OV) and carcass (CA). By contrast, by day 7 of feeding, the AamOatp mRNA was 60-80-fold more strongly expressed in the OV than in the SG, MG and CA. These data strongly indicate that changing physiological needs during the tick feeding process influences transcriptional regulation of AamOatp. Our data also show that RNAi-mediated suppression of the AamOatp caused ticks to obtain smaller blood meals, which consequently resulted in ticks laying fewer eggs. The results are discussed in the context of AamOatp as a potential pharmacological or anti-tick vaccine target.

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“…Annotating these genomes and distributing the results for the benefit of the larger biomedical community is proving difficult for many of these communities, as they often lack bioinformatics experience. One solution to this problem is to outsource the annotation to one of the major annotation databases such as Ensembl (Stabenau et al 2004) or VectorBase (Lawson et al 2007). This has proven a fruitful strategy for several groups (c.f.…”

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confidence: 99%

“…broad.mit.edu/tools/software.html; http://www.tigr.org/ software/genefinding.shtml) (Stabenau et al 2004). However this is not their primary mission, and they usually only make subsets of their internal systems available-and these generally require significant in-house bioinformatics support (Lawson et al 2007). Thus, despite the best efforts of the bioinformatics community, large numbers of unannotated genomes continue to accumulate, underscoring an urgent need for simpler, more portable annotation pipelines.…”

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confidence: 99%

MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes

et al. 2007

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We have developed a portable and easily configurable genome annotation pipeline called MAKER. Its purpose is to allow investigators to independently annotate eukaryotic genomes and create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab initio gene predictions, and automatically synthesizes these data into gene annotations having evidence-based quality indices. MAKER is also easily trainable: Outputs of preliminary runs are used to automatically retrain its gene-prediction algorithm, producing higher-quality gene-models on subsequent runs. MAKER’s inputs are minimal, and its outputs can be used to create a GMOD database. Its outputs can also be viewed in the Apollo Genome browser; this feature of MAKER provides an easy means to annotate, view, and edit individual contigs and BACs without the overhead of a database. As proof of principle, we have used MAKER to annotate the genome of the planarian Schmidtea mediterranea and to create a new genome database, SmedGD. We have also compared MAKER’s performance to other published annotation pipelines. Our results demonstrate that MAKER provides a simple and effective means to convert a genome sequence into a community-accessible genome database. MAKER should prove especially useful for emerging model organism genome projects for which extensive bioinformatics resources may not be readily available.

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VectorBase: a home for invertebrate vectors of human pathogens

Cited by 112 publications

References 13 publications

Four years of DNA barcoding: Current advances and prospects

Four years of DNA barcoding: Current advances and prospects

Molecular and biological characterization of the Amblyomma americanum organic anion transporter polypeptide

MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes

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