MatGAT: An application that generates similarity/identity matrices using protein or DNA sequences

Campanella, James J.; Bitincka, Ledion; Smalley, John V.

doi:10.1186/1471-2105-4-29

Cited by 759 publications

(184 citation statements)

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“…1A). Amino acid sequence comparison using MatGat software (31) indicated that chIL-17RA shared ca. 46% identity with its human, mouse, and rat counterparts and 29.2 to 31.5% identity with trout, salmon, and zebrafish.…”

Section: Resultsmentioning

confidence: 99%

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Downregulation of Chicken Interleukin-17 Receptor A during Eimeria Infection

et al. 2014

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e Both interleukin-17A (IL-17A) and IL-17F are proinflammatory cytokines that have an important role in intestinal homeostasis via receptor signaling. These cytokines have been characterized in chickens, but very little is known about their receptors and their functional activity. We provide here the first description of the sequence analysis, bioactivity, and comparative expression analysis of chicken IL-17RA (chIL-17RA) in chickens infected with Salmonella and Eimeria, two major infectious agents of gastrointestinal diseases of poultry of economic importance. A full-length chIL-17RA cDNA with a 2,568-bp coding region was identified from chicken thymus cDNA. chIL-17RA shares ca. 46% identity with mammalian homologues and 29.2 to 31.5% identity with its piscine counterparts. chIL-17RA transcript expression was relatively high in the thymus and in the chicken macrophage cell line HD11. The chIL-17RA-specific small interfering RNA inhibits interleukin-6 (IL-6), IL-8, and IL-1␤ mRNA expression in chicken embryo fibroblast cells (but not in DF-1 cells) stimulated with chIL-17A or chIL-17F. Interaction between chIL-17RA and chIL-17A was confirmed by coimmunoprecipitation. Downregulation of chIL-17RA occurred in concanavalin A-or lipopolysaccharide-activated splenic lymphocytes but not in poly(I·C)-activated splenic lymphocytes. In Salmonella-and Eimeria-infected chickens, the expression levels of the chIL-17RA transcript were downregulated in intestinal tissues from chickens infected with two Eimeria species, E. tenella or E. maxima, that preferentially infect the cecum and jejunum, respectively. However, chIL-17RA expression was generally unchanged in Salmonella infection. These results suggest that chIL-17RA has an important role in mucosal immunity to intestinal intracellular parasite infections such as Eimeria infection.

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Section: Resultsmentioning

confidence: 99%

“…Prediction of disulfide bond partners was performed using DiANNA 1.1 software (30). Homology analysis was performed using MatGat software (31).…”

Section: Animals and Infectionsmentioning

confidence: 99%

Downregulation of Chicken Interleukin-17 Receptor A during Eimeria Infection

et al. 2014

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“…This software, provided as a supplement package by Deloger et al (31), was then used to trim the overlapping MUMs and to generate MUM index (MUMi) values for the genome relatedness comparison. The similarity/identity matrix between all 16S and 23S rRNA bifidobacterial gene sequences was calculated with MatGat, version 2.03 (Matrix Global Alignment Tool), using the BLOSUM 50 alignment matrix (32).…”

Section: Methodsmentioning

confidence: 99%

Investigation of the Evolutionary Development of the Genus Bifidobacterium by Comparative Genomics

Lugli

Milani

Turroni

et al. 2014

Appl Environ Microbiol

116

121

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The Bifidobacterium genus currently encompasses 48 recognized taxa, which have been isolated from different ecosystems. However, the current phylogeny of bifidobacteria is hampered by the relative paucity of genotypic data. Here, we reassessed the taxonomy of this bacterial genus using genome-based approaches, which demonstrated that the previous taxonomic view of bifidobacteria contained several inconsistencies. In particular, high levels of genetic relatedness were shown to exist between particular Bifidobacterium taxa which would not justify their status as separate species. The results presented are here based on average nucleotide identity analysis involving the genome sequences for each type strain of the 48 bifidobacterial taxa, as well as phylogenetic comparative analysis of the predicted core genome of the Bifidobacterium genus. The results of this study demonstrate that the availability of complete genome sequences allows the reconstruction of a more robust bifidobacterial phylogeny than that obtained from a single gene-based sequence comparison, thus discouraging the assignment of a new or separate bifidobacterial taxon without such a genome-based validation.

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“…Signal peptide predictions were made using Signal P4.0 software (http://www.cbs.dtu.dk/services/SignalP) according to Petersen et al (42), and N-glycosylation sites were predicted using the NetNGlyc 1.0 server (http://www.cbs.dtu.dk/services/NetNGlyc) (R. Gupta, E. Jung, and S. Brunak, unpublished data). Amino acid homology comparisons were performed using the MatGAT package (version 2.02) (43). Phylogenetic trees were constructed from CLUSTAL W-generated alignments using the neighbor-joining (N-J) method within the MEGA (version 4.1) package (44).…”

Section: Methodsmentioning

confidence: 99%