A Number Of Thoughts On The Foreseeable Future Of the Thalidomide

Graphs are ... (i) Metagenome-level metrics (Table ?(Table1).1). The following metrics are defined to provide a comparison between different metagenomes based on the abundance and distribution of sequences similar to characterized phages that they contain. First, all metagenomic sequence reads with significant tBLASTX hits to phage sequences were collected from Eco-Locator recruitment plots and stored for further calculations. Those values were counted and defined as nHits. Default significance thresholds were set at BLAST E-values of 10?5. Next, an abundance index (AI) was calculated for each metagenome. For a given metagenome, Non-specific serine/threonine protein kinase the AI was defined as the number of hits to phage genomes (nHits) normalized to the metagenome size in millions of base pairs. AI=nHits/metagenome?size,?Mbp Subsequently, a total abundance index was defined for each metagenome to express the overall abundance of sequences with similarities to characterized phage genomes in that metagenome. Total?abundance?index?(of?all?phage?genomes)?per?metagenome???????????????????????????????????????????????????=��(nHits/metagenome?size,?Mbp) Because of the high variability of phage types in different ecosystems, the total AI defined above is highly sensitive to outliers, and thus the median AI of sequences with similarities to characterized phage genomes per metagenome was calculated as another useful value to compare metagenomes and reflect their phage content. In addition to AI and median AI, which reflect phage-like Crizotinib purchase metagenomic ROCK inhibitor fragment counts, we also used some commonly used ecological biodiversity parameters such as richness, diversity, and evenness, described elsewhere (Shannon, 1948 disambiguated in Spellerberg and Fedor, 2003). A full list of metagenome-level metrics, and the significance of each, is provided in Table ?Table11. (ii) Phage genome-level metrics. Inter-phage properties (Table ?(Table2).2). For comparison of phage genomes, a phage abundance index (PAI) was defined for each phage and calculated as the number of metagenomic sequence fragments assignable to that phage genome normalized to the genome size PAI=��?AI/Phage?genome?length?(Kbp) Because PAI depends on summing up all available metagenomic sequences that are similar to a particular phage, this value reflects a phage's overall abundance in a set of ecosystems, but provides little information about the pattern of its distribution, since a very high PAI may be contributed by an overabundance in a small number of metagenomes (nMGs). Instead, an estimation of the distribution of a certain phage in a given set of ecosystems may be expressed as a simple count of the nMGs with significant BLAST hits (E-value