ChemGenome2.1: An Ab Initio Gene Prediction Software

Mishra, Aashwin; Siwach, Priyanka; Singhal, Poonam; Jayaram, B.

doi:10.1007/978-1-4939-9173-0_7

Cited by 2 publications

(1 citation statement)

References 39 publications

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“…iPtgxDBs were generated based on the S. meliloti 2011 ASM34606v1 reference genome sequence as described (Omasits et al 2017 ). Annotations from several reference genome centers and/or releases (GenBank 2014, RefSeq2017 , Genoscope), two ab initio gene predictions (Prodigal, Hyatt et al 2010 ; ChemGenome, Mishra et al 2019 ), and in silico ORF predictions were hierarchically integrated for a trypsin-specific iPtgxDB as previously detailed (Melior et al 2020 ), ( https://iptgxdb.expasy.org/database/annotations/s-meliloti-tryptic; see Table S3.1). To capture data from all three experimental approaches, two more iPtgxDBs were created in a similar fashion using command-line utilities.…”

Section: Methodsmentioning

confidence: 99%

Unraveling the small proteome of the plant symbiontSinorhizobium melilotiby ribosome profiling and proteogenomics

et al. 2023

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The soil-dwelling plant symbiont Sinorhizobium meliloti is a major model organism of Alphaproteobacteria. Despite numerous detailed OMICS studies, information about small open reading frame (sORF)-encoded proteins (SEPs) is largely missing, because sORFs are poorly annotated and SEPs are hard to detect experimentally. However, given that SEPs can fulfill important functions, identification of translated sORFs is critical for analyzing their roles in bacterial physiology. Ribosome profiling (Ribo-seq) can detect translated sORFs with high sensitivity, but is not yet routinely applied to bacteria because it must be adapted for each species. Here, we established a Ribo-seq procedure for S. meliloti 2011 based on RNase I digestion and detected translation for 60% of the annotated coding sequences during growth in minimal medium. Using ORF prediction tools based on Ribo-seq data, subsequent filtering, and manual curation, the translation of 37 non-annotated sORFs with ≤ 70 amino acids was predicted with confidence. The Ribo-seq data were supplemented by mass spectrometry (MS) analyses from three sample preparation approaches and two integrated proteogenomic search database (iPtgxDB) types. Searches against standard and 20-fold smaller Ribo-seq data-informed custom iPtgxDBs confirmed 47 annotated SEPs and identified 11 additional novel SEPs. Epitope tagging and Western blot analysis confirmed the translation of 15 out of 20 SEPs selected from the translatome map. Overall, by combining MS and Ribo-seq approaches, the small proteome of S. meliloti was substantially expanded by 48 novel SEPs. Several of them are part of predicted operons and/or are conserved from Rhizobiaceae to Bacteria, suggesting important physiological functions.

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Section: Methodsmentioning

confidence: 99%

Unraveling the small proteome of the plant symbiontSinorhizobium melilotiby ribosome profiling and proteogenomics

et al. 2023

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Intron exon boundary junctions in human genome have in-built unique structural and energetic signals

Mishra

Siwach

Misra

et al. 2021

Nucleic Acids Research

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Precise identification of correct exon–intron boundaries is a prerequisite to analyze the location and structure of genes. The existing framework for genomic signals, delineating exon and introns in a genomic segment, seems insufficient, predominantly due to poor sequence consensus as well as limitations of training on available experimental data sets. We present here a novel concept for characterizing exon–intron boundaries in genomic segments on the basis of structural and energetic properties. We analyzed boundary junctions on both sides of all the exons (3 28 368) of protein coding genes from human genome (GENCODE database) using 28 structural and three energy parameters. Study of sequence conservation at these sites shows very poor consensus. It is observed that DNA adopts a unique structural and energy state at the boundary junctions. Also, signals are somewhat different for housekeeping and tissue specific genes. Clustering of 31 parameters into four derived vectors gives some additional insights into the physical mechanisms involved in this biological process. Sites of structural and energy signals correlate well to the positions playing important roles in pre-mRNA splicing.

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ChemGenome2.1: An Ab Initio Gene Prediction Software

Cited by 2 publications

References 39 publications

Unraveling the small proteome of the plant symbiontSinorhizobium melilotiby ribosome profiling and proteogenomics

Unraveling the small proteome of the plant symbiontSinorhizobium melilotiby ribosome profiling and proteogenomics

Intron exon boundary junctions in human genome have in-built unique structural and energetic signals

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