Choosing BLAST options for better detection of orthologs as reciprocal best hits

Moreno–Hagelsieb, Gabriel; Latimer, Kristen

doi:10.1093/bioinformatics/btm585

Cited by 449 publications

(374 citation statements)

References 33 publications

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“…When the BLAST searches of genome data described above returned significant "hits", the sequences obtained were then reciprocally searched against the NCBI protein database by BLAST to confirm the validity of the sequences retrieved with the initial search (58). To identify distant homologs that might have escaped these simple searches, two additional methods were used.…”

Section: Methodsmentioning

confidence: 99%

Ancient origin of the integrin-mediated adhesion and signaling machinery

Sebé-Pedrós

Roger

Lang

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

229

276

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The evolution of animals (metazoans) from their unicellular ancestors required the emergence of novel mechanisms for cell adhesion and cell-cell communication. One of the most important cell adhesion mechanisms for metazoan development is integrinmediated adhesion and signaling. The integrin adhesion complex mediates critical interactions between cells and the extracellular matrix, modulating several aspects of cell physiology. To date this machinery has been considered strictly metazoan specific. Here we report the results of a comparative genomic analysis of the integrin adhesion machinery, using genomic data from several unicellular relatives of Metazoa and Fungi. Unexpectedly, we found that core components of the integrin adhesion complex are encoded in the genome of the apusozoan protist Amastigomonas sp., and therefore their origins predate the divergence of Opisthokonta, the clade that includes metazoans and fungi. Furthermore, our analyses suggest that key components of this apparatus have been lost independently in fungi and choanoflagellates. Our data highlight the fact that many of the key genes that had formerly been cited as crucial for metazoan origins have a much earlier origin. This underscores the importance of gene cooption in the unicellular-to-multicellular transition that led to the emergence of the Metazoa.cell adhesion | lateral gene transfer | metazoan origins | multicellularity

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Section: Methodsmentioning

confidence: 99%

Ancient origin of the integrin-mediated adhesion and signaling machinery

Sebé-Pedrós

Roger

Lang

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

229

276

View full text Add to dashboard Cite

show abstract

“…Error bars indicate standard deviation. n = 8 except for prevtg n = 6. microarray used in the present study and the Agilent zebrafish microarray (product 015064) used in the previous work were identified using a reciprocal best hit approach (Moreno-Hagelsieb and Latimer, 2008). In total, 9171 homologous features (not all unique) were identified.…”

Section: Microarray Data Analysismentioning

confidence: 99%

Influence of ovarian stage on transcript profiles in fathead minnow (Pimephales promelas) ovary tissue

et al. 2010

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“…Orthologs were detected ( Figure 1A) using the BLAST reciprocal best hit method [22]. All six possible BLAST pairwise species sequence comparisons were completed in both directions (speciesX vs speciesY and speciesY vs. SpeciesX) and the resulting tab-delimited output files were loaded into the open source MySQL relational database (https:// www.mysql.com/).…”

Section: Ortholog Detectionmentioning

confidence: 99%

Leveraging Naked Mole Rat (Heterocephalus glaber) Comparative Genomics to Identify Canine Genes Modulating Susceptibility to Tumorigenesis and Cancer Phenotypes

Irizarry¹,

Punt²

2015

J Veterinar Sci Technol

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We utilized a comparative genomics approach to analyze a core set of tumorigenesis orthologs among human, mouse, dog and naked mole rat. The analysis identified cancer orthologs that are both conserved and divergent between dog and the cancer resistant species naked mole rat. These tumorigenesis orthologous are associated with phenotypes that modulate cancer susceptibility, cardiac development, craniofacial development, brain development, skeletal development, and immune function, to name a few. This bioinformatics approach employed a variety of literature mining tools to further uncover relationships between the tumorigenesis orthologs. Together, these results shed light on the relationship between breed formations, breed associated morphological traits and breed associated susceptibility to tumorigenesis. These findings support the use of a comparative genomic analysis between species with dramatically different disease phenotypes as a gene discovery tool. A total of 146 proteins coding SNPs were identified in these tumorigenesis orthologs representing missense variations, frame shift variations and nonsense variations. The genes identified in this study can serve as a list of candidates for subsequent laboratory and clinical study. Furthermore, the identification of SNPs impacting the primary structure of the tumorigenesis orthologs may provide clues about the basis of cancer susceptibility between dog breeds.

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Choosing BLAST options for better detection of orthologs as reciprocal best hits

Abstract: Orthologs detected as Reciprocal Best Hits using soft masking and Smith-Waterman alignments can be downloaded from http://popolvuh.wlu.ca/Orthologs.

Cited by 449 publications

References 33 publications

Ancient origin of the integrin-mediated adhesion and signaling machinery

Ancient origin of the integrin-mediated adhesion and signaling machinery

Influence of ovarian stage on transcript profiles in fathead minnow (Pimephales promelas) ovary tissue

Leveraging Naked Mole Rat (Heterocephalus glaber) Comparative Genomics to Identify Canine Genes Modulating Susceptibility to Tumorigenesis and Cancer Phenotypes

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