Hidden markov model for the prediction of transmembrane proteins using MATLAB

Chaturvedi, Navaneet; Shanker, Sudhanshu; Singh, Vinay Kumar; Sinha, Durganand; Pandey, P. N.

doi:10.6026/97320630007418

Cited by 4 publications

(2 citation statements)

References 8 publications

(19 reference statements)

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“…Multiple alignments of amino acid sequences were generated using the Multiple Alignment Module of LaserGene of DNASTAR software® (DNASTAR, Inc.). The Simple Modular Architecture Research Tool (SMART) [ 20 ] and the Transmembrane Hidden Markov Model package 2 (TMHMM2) [ 21 ] were used to predict domains and signal peptides in the RmAQP2 protein sequences. The tools Transmembrane Protein Representation in 2 Dimensions (TMRPres2) [ 22 ] and Swiss-model [ 23 ] were used to create 2D and 3D (respectively) visual representations of the RmAQP2 protein for topology analyses.…”

Section: Methodsmentioning

confidence: 99%

Targeted silencing of the Aquaporin 2 gene of Rhipicephalus (Boophilus) microplus reduces tick fitness

et al. 2015

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BackgroundTicks are blood-feeding arthropods that can affect human and animal health both directly by blood-feeding and indirectly by transmitting pathogens. The cattle tick Rhipicephalus (Boophilus) microplus is one of the most economically important ectoparasites of bovines worldwide and it is responsible for the transmission of the protozoan Babesia bovis, the etiological agent of bovine babesiosis. Aquaporins (AQPs) are water channel proteins implicated in physiological mechanisms of osmoregulation. Members of the AQP family are critical for blood-feeding arthropods considering the extreme osmoregulatory changes that occur during their feeding. We investigated the pattern of expression of a newly identified AQP2 gene of R. microplus (RmAQP2) in different tick tissues and stages. We also examined in vivo the biological implications of silencing expression of RmAQP2 silencing during tick feeding on either uninfected or B. bovis-infected cattle.MethodsIn silico gene analyses were performed by multiple alignments of amino acid sequences and topology prediction. Levels of RmAQP2 transcripts in different tick tissues and stages were analyzed by reverse transcriptase quantitative PCR. Patterns of expression of RmAQP2 protein were investigated by immunoblots. Gene silencing was performed by RNA interference and in vivo functional analyses carried out by feeding ticks on either uninfected or B. bovis-infected cattle.ResultsRmAQP2 transcripts were found in unfed larvae, engorged nymphs, and salivary glands and guts of partially engorged females; however, of all tick tissues and stages examined, RmAQP2 protein was found only in salivary glands of partially engorged females. RmAQP2 silencing significantly reduced tick fitness and completely abrogated protein expression. The effect of RmAQP2 silencing on fitness was more pronounced in females fed on a B. bovis-infected calf than in ticks fed on an uninfected calf and none of their larval progeny survived.ConclusionsCollectively, considering the gene expression and tick fitness data, we conclude that RmAQP2 is critical for tick blood feeding and may be a suitable candidate target for the development of novel strategies to control R. microplus and tick-borne parasites.Electronic supplementary materialThe online version of this article (doi:10.1186/s13071-015-1226-2) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Targeted silencing of the Aquaporin 2 gene of Rhipicephalus (Boophilus) microplus reduces tick fitness

et al. 2015

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“…Taken all the data together, 5222 proteins were retrieved. Panther and PFamCrossReference were also used as a collection of protein families compiled using multiple sequence alignments and hidden Markov models [ 94 ]. Pfam and GO information were saved in an excel file expanded to include available protein information in Uniprot - Swiss TrEMBL database and related API information linked.…”

Section: Methodsmentioning

confidence: 99%

Developing a bioinformatics pipeline for comparative protein classification analysis

Pelosi

2022

BMC Genom Data

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Background Protein classification is a task of paramount importance in various fields of biology. Despite the great momentum of modern implementation of protein classification, machine learning techniques such as Random Forest and Neural Network could not always be used for several reasons: data collection, unbalanced classification or labelling of the data.As an alternative, I propose the use of a bioinformatics pipeline to search for and classify information from protein databases. Hence, to evaluate the efficiency and accuracy of the pipeline, I focused on the carotenoid biosynthetic genes and developed a filtering approach to retrieve orthologs clusters in two well-studied plants that belong to the Brassicaceae family: Arabidopsis thaliana and Brassica rapa Pekinensis group. The result obtained has been compared with previous studies on carotenoid biosynthetic genes in B. rapa where phylogenetic analysis was conducted. Results The developed bioinformatics pipeline relies on commercial software and multiple databeses including the use of phylogeny, Gene Ontology terms (GOs) and Protein Families (Pfams) at a protein level. Furthermore, the phylogeny is coupled with “population analysis” to evaluate the potential orthologs. All the steps taken together give a final table of potential orthologs. The phylogenetic tree gives a result of 43 putative orthologs conserved in B. rapa Pekinensis group. Different A. thaliana proteins have more than one syntenic ortholog as also shown in a previous finding (Li et al., BMC Genomics 16(1):1–11, 2015). Conclusions This study demonstrates that, when the biological features of proteins of interest are not specific, I can rely on a computational approach in filtering steps for classification purposes. The comparison of the results obtained here for the carotenoid biosynthetic genes with previous research confirmed the accuracy of the developed pipeline which can therefore be applied for filtering different types of datasets.

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Insights into the gene and protein structures of the CaSWEET family members in chickpea (Cicer arietinum), and their gene expression patterns in different organs under various stress and abscisic acid treatments

Chu

Tran

et al. 2022

Gene

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Hidden markov model for the prediction of transmembrane proteins using MATLAB

Cited by 4 publications

References 8 publications

Targeted silencing of the Aquaporin 2 gene of Rhipicephalus (Boophilus) microplus reduces tick fitness

Targeted silencing of the Aquaporin 2 gene of Rhipicephalus (Boophilus) microplus reduces tick fitness

Developing a bioinformatics pipeline for comparative protein classification analysis

Insights into the gene and protein structures of the CaSWEET family members in chickpea (Cicer arietinum), and their gene expression patterns in different organs under various stress and abscisic acid treatments

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