دورية أكاديمية
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A knowledge-driven protocol for prediction of proteins of interest with an emphasis on biosynthetic pathways.

التفاصيل البيبلوغرافية
العنوان: A knowledge-driven protocol for prediction of proteins of interest with an emphasis on biosynthetic pathways.
المؤلفون: Joshi AG; National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India., Harini K; National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India., Meenakshi I; National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India., Shafi KM; National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India.; The University of Trans-Disciplinary Health Sciences and Technology (TDU), Yelahanka, Bangalore 560064, Karnataka, India., Pasha SN; National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India., Mahita J; National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India., Sajeevan RS; National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India., Karpe SD; National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India., Ghosh P; National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India., Nitish S; National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India.; The University of Trans-Disciplinary Health Sciences and Technology (TDU), Yelahanka, Bangalore 560064, Karnataka, India., Gandhimathi A; National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India., Mathew OK; National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India., Prasanna SH; National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India., Malini M; National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India., Mutt E; National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India., Naika M; National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India., Ravooru N; National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India., Rao RM; National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India., Shingate PN; National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India., Sukhwal A; National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India., Sunitha MS; National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India., Upadhyay AK; National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India.; Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147004, Punjab, India., Vinekar RS; National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India., Sowdhamini R; National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India.
المصدر: MethodsX [MethodsX] 2020 Sep 02; Vol. 7, pp. 101053. Date of Electronic Publication: 2020 Sep 02 (Print Publication: 2020).
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Elsevier B.V Country of Publication: Netherlands NLM ID: 101639829 Publication Model: eCollection Cited Medium: Print ISSN: 2215-0161 (Print) Linking ISSN: 22150161 NLM ISO Abbreviation: MethodsX Subsets: PubMed not MEDLINE
أسماء مطبوعة: Original Publication: Amsterdam : Elsevier B.V., [2014]-
مستخلص: This protocol describes a stepwise process to identify proteins of interest from a query proteome derived from NGS data. We implemented this protocol on Moringa oleifera transcriptome to identify proteins involved in secondary metabolite and vitamin biosynthesis and ion transport. This knowledge-driven protocol identifies proteins using an integrated approach involving sensitive sequence search and evolutionary relationships. We make use of functionally important residues (FIR) specific for the query protein family identified through its homologous sequences and literature. We screen protein hits based on the clustering with true homologues through phylogenetic tree reconstruction complemented with the FIR mapping. The protocol was validated for the protein hits through qRT-PCR and transcriptome quantification. Our protocol demonstrated a higher specificity as compared to other methods, particularly in distinguishing cross-family hits. This protocol was effective in transcriptome data analysis of M. oleifera as described in Pasha et al.•Knowledge-driven protocol to identify secondary metabolite synthesizing protein in a highly specific manner.•Use of functionally important residues for screening of true hits.•Beneficial for metabolite pathway reconstruction in any (species, metagenomics) NGS data.
Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
(© 2020 The Authors. Published by Elsevier B.V.)
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فهرسة مساهمة: Keywords: CHI, Chalcone Flavanone Isomerase; DEPC, Diethyl Pyrocarbonate, GAPDH, Glyceraldehyde-3-phosphate dehydrogenase gene; FIR, Functionally Important Residue; Functionally important residue; Homology; MSA, Multiple Sequence Alignment; Multiple sequence alignment; PIM, Percentage Identity Matrix; Pathway; Phylogenetic analysis
تواريخ الأحداث: Date Created: 20201007 Latest Revision: 20201009
رمز التحديث: 20240829
مُعرف محوري في PubMed: PMC7528181
DOI: 10.1016/j.mex.2020.101053
PMID: 33024710
قاعدة البيانات: MEDLINE
الوصف
تدمد:2215-0161
DOI:10.1016/j.mex.2020.101053