<i>Astraptes</i> MOTU.

<p><i>Astraptes</i> MOTU.</p

Handbook on the geographies of regions and territories

Handbook on the geographies of regions and territorie

Outline of the jMOTU and Taxonerator pipeline.

<p>A: The jMOTU-Taxonerator workflow. The labelled grey boxes indicate the portions of the pipeline carried out by each program. Within jMOTU, input sequences are preclustered to remove exact subsequences, and representative sequences chosen for each precluster. Pairwise megablast scores are calculated for representative sequences, and exact distances between highly similar pairs are calculated using NW alignment. These exact distances are used to cluster the representative sequences into MOTU at various distance cutoff values. Within Taxonerator, each MOTU is processed separately. A representative sequence is chosen and used as the query in a megablast search of a preformatted database. The top 10 hits are extracted and their taxonomic hierarchy is stored for further analysis. B: The structure of the jMOTU (upper part) and Taxonerator (lower part, boxed)SQL database.</p

Beach meiofaunal ecosystem survey.

<p>Beach meiofaunal ecosystem survey.</p

MOTU inferred in 1081 <i>Astraptes</i> cytochrome oxidase 1 sequences.

<p>MOTU were inferred using jMOTU at a range of cutoffs (x-axis). There were 162 0 bp MOTU, and 32 2 bp MOTU.</p

jMOTU and Taxonerator in action.

<p>Screeshots of (above) jMOTU's parameter pane, and display of MOTU numbers versus cutoff, and (below) Taxonerator's interactive data entry panel.</p

Analysis of community-sampled Roche 454 pyrosequencing barcode data.

<p>A 292,397-sequence dataset of nuclear small subunit ribosomal RNA gene fragments <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019259#pone.0019259-Creer1" target="_blank">[9]</a> was analysed using jMOTU and Taxonerator. A: For the 9 samples making up the dataset, the number of MOTU defined (y-axis; note log scale) at each base pair cutoff (x-axis) is shown. B: The numbers of 4 base MOTU inferred from each sample independently, and from the combined analysis of all representative sequences from each sample's 3 base MOTU. The stacked histogram bars indicate the assignment of these MOTU to animal phyla and other major taxa using Taxonerator (the key to colouration is in the lower right of the figure, and single-letter identifications for the major metazoan phyla are overlaid). C: Proportional presence in each sample of original sequences deriving from different animal phyla and other major taxa using Taxonerator annotations of the combined analysis 4 base MOTU (the key to colouration is in the lower right of the figure, and single-letter identifications for the major metazoan phyla are overlaid).</p

Standard tournament: Mean score per turn of top 15 strategies (ranked by median over 50000 tournaments).

<p>The leaderboard is dominated by the trained strategies (indicated by a *).</p

Standard tournament: Mean score per turn of top 15 strategies (ranked by median over 50000 tournaments).

<p>The leaderboard is dominated by the trained strategies (indicated by a *).</p

Standard tournament: Mean score per turn (strategies ordered by median score over 50000 tournaments).

<p>Standard tournament: Mean score per turn (strategies ordered by median score over 50000 tournaments).</p