Open Access Highly Accessed Research article

Rapid phylogenetic and functional classification of short genomic fragments with signature peptides

Joel Berendzen1, William J Bruno2, Judith D Cohn3, Nicolas W Hengartner3, Cheryl R Kuske4, Benjamin H McMahon2*, Murray A Wolinsky4 and Gary Xie4

Author Affiliations

1 Physics Division, MS D454, Los Alamos National Laboratory, Los Alamos, NM 87545, USA

2 Theoretical Division, MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA

3 Computer, Computational, and Statistical Sciences Division, MS B256, Los Alamos National Laboratory, Los Alamos, NM 87545, USA

4 Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA

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BMC Research Notes 2012, 5:460  doi:10.1186/1756-0500-5-460

Published: 28 August 2012

Additional files

Additional file 1:

List of 10-mer matches. This file contains a tabdelimited text table of 10-mer or longer matches between E. coli and Bacillus subtilis, with the annotation and amino acid sequence of the genes containing the match.

Format: TXT Size: 1.8MB Download file

Open Data

Additional file 2:

Phylogenetic tree with node numbers. This file contains a pdf file of the phylogenetic tree of the 403 reference bacterial genomes used to assign phylogeny to both signatures and metagenomic reads. Node numbers are provide for use in Additional file 5.

Format: PDF Size: 37KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

Phylogenetic tree with node numbers.This file contains a phyloxml file of the phylogenetic tree of the 403 reference bacterial genomes used to assign phylogeny to both signatures and metagenomic reads. Node numbers are provide for use in Additional file 5.

Format: PHYLOXML Size: 813KB Download file

Open Data

Additional file 4:

Synthetic data produced from draft genomes of four soil bacteria. This file contains a zip file of the 16 synthetic data sets used to compare sensitivity, specificity, and throughput of our method to three types of BLAST-based methods. (TAR 6400 kb)

Format: TAR Size: 6.2MB Download file

Open Data

Additional file 5:

Phylogenetic profile of metagenomic samples. This file contains a tab-delimited text table of the number of reads assigned to each node on the phylogenetic tree for each sample. Node numbers refer to the phylogenetic tree shown in Additional file 1 and Additional file 2. (TXT 13 kb)

Format: TXT Size: 14KB Download file

Open Data

Additional file 6:

Functional profile of metagenomic samples. This file contains a tab-delimited text table of the number of reads assigned to each of the 1088 SEED categories, for each sample. (TXT 91 kb)

Format: TXT Size: 92KB Download file

Open Data

Additional file 7:

Reference genomes. This file contains a tab-delimited text table of reference genomes used, with source for each. (TXT 32 kb)

Format: TXT Size: 33KB Download file

Open Data