Work

Phylogenetic diversity of metagenome assembled genomes (MAGs) from bank vole (Myodes glareolus) gut microbiota.

Year: 2020

Type: dataset

Abstract: Concatenated alignment of 16 ribosomal proteins (L2, L3, L4, L5, L6, L14, L16, L18, L22, L24, S3, S8, S10, S17 and S19) identified in bank vole (Myodes glareolus) gut bacteria (metagenome assembled genomes, MAGs) and bacterial reference genomes obtained from Genbank. Data were obtained by (1) searching for the 16 phylogenetic markers from the MAGs and the reference genomes using HMMSEARCH43 in HMMER v.3.1b2, then (2) aligning data using MUSCLE45 v.3.8.31, (3) trimming the alignments using TRIMAL46 v.1.2rev59, and (4) concatenating the alignments using the CONCAT script implemented by BINSANITY. A detailed protocol for this phylogenomic workflow can be found at ProtocolsIO (dx.doi.org/10.17504/protocols.io.mp5c5q6).

Source: Figshare

DOI: 10.6084/m9.figshare.12085881

Authors: Knight, Rob, Mousseau, Timothy A, Mappes, Tapio, Tukalenko, Eugene, Watts, Phillip, Lavrinienko, Anton, Thompson, Luke

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

OpenAlex ID: W4394440939

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