Dataset Information

Beyond sequencing: re-visiting annotations for PJL as a test case.

ABSTRACT: OBJECTIVES:Current developments in sequencing techniques have enabled rapid and high-throughput generation of sequence data. However, there is a growing gap between the generation of raw sequencing data and the extraction of meaningful biological information. Variant annotation is a crucial step in the analysis of genome sequencing data. Incorrect or incomplete annotations can cause researchers to dilute interesting variants in a pool of false positives. We require consistent, accurate and reliable annotation of variants for making diagnostic and treatment decisions. Current annotation depends on the set of transcripts, and software used can be managed, with sufficient care, in the research context. Careful thought needs to be given to the choice of transcript sets and software packages for variant annotation in sequencing studies. In this project, the main objective is to analyze the genetic variants observed in Pakistani population data within the 1000 genomes project (1KGP). RESULTS:We characterized only SNVs and InDels types of genetic variations, in total?~?1.4 million variants. Besides this, we also annotated the genetic variants with multiple annotations tools, ANNOVAR and SnpEff and compared the differential results. Our population-specific catalogue will enhance future studies on the functional impact at protein level.

SUBMITTER: Khan W

PROVIDER: S-EPMC6670121 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Beyond sequencing: re-visiting annotations for PJL as a test case.

Khan Waqasuddin W Ghani Aisha A Azmi Muhammad Bilal MB Razzak Safina Abdul SA

BMC research notes 20190731 1

<h4>Objectives</h4>Current developments in sequencing techniques have enabled rapid and high-throughput generation of sequence data. However, there is a growing gap between the generation of raw sequencing data and the extraction of meaningful biological information. Variant annotation is a crucial step in the analysis of genome sequencing data. Incorrect or incomplete annotations can cause researchers to dilute interesting variants in a pool of false positives. We require consistent, accurate a ...[more]

PMID: 31366397

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Project description:BackgroundPrecise DNA-protein interactions play most important and vital role in maintaining the normal physiological functioning of the cell, as it controls many high fidelity cellular processes. Detailed study of the nature of these interactions has paved the way for understanding the mechanisms behind the biological processes in which they are involved. Earlier in 2000, a systematic classification of DNA-protein complexes based on the structural analysis of the proteins was proposed at two tiers, namely groups and families. With the advancement in the number and resolution of structures of DNA-protein complexes deposited in the Protein Data Bank, it is important to revisit the existing classification.ResultsOn the basis of the sequence analysis of DNA binding proteins, we have built upon the protein centric, two-tier classification of DNA-protein complexes by adding new members to existing families and making new families and groups. While classifying the new complexes, we also realised the emergence of new groups and families. The new group observed was where β-propeller was seen to interact with DNA. There were 34 SCOP folds which were observed to be present in the complexes of both old and new classifications, whereas 28 folds are present exclusively in the new complexes. Some new families noticed were NarL transcription factor, Z-α DNA binding proteins, Forkhead transcription factor, AP2 protein, Methyl CpG binding protein etc.ConclusionsOur results suggest that with the increasing number of availability of DNA-protein complexes in Protein Data Bank, the number of families in the classification increased by approximately three fold. The folds present exclusively in newly classified complexes is suggestive of inclusion of proteins with new function in new classification, the most populated of which are the folds responsible for DNA damage repair. The proposed re-visited classification can be used to perform genome-wide surveys in the genomes of interest for the presence of DNA-binding proteins. Further analysis of these complexes can aid in developing algorithms for identifying DNA-binding proteins and their family members from mere sequence information.

Dataset Information

Beyond sequencing: re-visiting annotations for PJL as a test case.

Publications

Beyond sequencing: re-visiting annotations for PJL as a test case.

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