Dataset Information

Genomic Analysis of a Marine Bacterium: Bioinformatics for Comparison, Evaluation, and Interpretation of DNA Sequences.

ABSTRACT: A total of five highly related strains of an unidentified marine bacterium were analyzed through their short genome sequences (AM260709-AM260713). Genome-to-Genome Distance (GGDC) showed high similarity to Pseudoalteromonas haloplanktis (X67024). The generated unique Quick Response (QR) codes indicated no identity to other microbial species or gene sequences. Chaos Game Representation (CGR) showed the number of bases concentrated in the area. Guanine residues were highest in number followed by cytosine. Frequency of Chaos Game Representation (FCGR) indicated that CC and GG blocks have higher frequency in the sequence from the evaluated marine bacterium strains. Maximum GC content for the marine bacterium strains ranged 53-54%. The use of QR codes, CGR, FCGR, and GC dataset helped in identifying and interpreting short genome sequences from specific isolates. A phylogenetic tree was constructed with the bootstrap test (1000 replicates) using MEGA6 software. Principal Component Analysis (PCA) was carried out using EMBL-EBI MUSCLE program. Thus, generated genomic data are of great assistance for hierarchical classification in Bacterial Systematics which combined with phenotypic features represents a basic procedure for a polyphasic approach on unambiguous bacterial isolate taxonomic classification.

SUBMITTER: Rekadwad BN

PROVIDER: S-EPMC5108866 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Genomic Analysis of a Marine Bacterium: Bioinformatics for Comparison, Evaluation, and Interpretation of DNA Sequences.

Rekadwad Bhagwan N BN Gonzalez Juan M JM Khobragade Chandrahasya N CN

BioMed research international 20161101

A total of five highly related strains of an unidentified marine bacterium were analyzed through their short genome sequences (AM260709-AM260713). Genome-to-Genome Distance (GGDC) showed high similarity to <i>Pseudoalteromonas haloplanktis</i> (X67024). The generated unique Quick Response (QR) codes indicated no identity to other microbial species or gene sequences. Chaos Game Representation (CGR) showed the number of bases concentrated in the area. Guanine residues were highest in number follow ...[more]

PMID: 27882328

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Dataset Information

Genomic Analysis of a Marine Bacterium: Bioinformatics for Comparison, Evaluation, and Interpretation of DNA Sequences.

Publications

Genomic Analysis of a Marine Bacterium: Bioinformatics for Comparison, Evaluation, and Interpretation of DNA Sequences.

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