Differential abundance of predicted CDS found in the 501 selected sequences and the total predicted <i>P. infestans</i> CDS, based on KOG functional categories.

<p>The differential abundance (<i>y</i> axis) of predicted CDS to assignable categories (<i>x</i> axis) is shown. KOG categories are as follows (from: <a href="http://www.ncbi.nlm.nih.gov/COG/" target="_blank">http://www.ncbi.nlm.nih.gov/COG/</a>): J, Translation; A, RNA processing and modification; K, Transcription; L, Replication, recombination and repair; B, Chromatin structure and dynamics; D, Cell cycle control, cell division, chromosome partitioning; Y, Nuclear structure; V, Defense mechanisms; T, Signal transduction mechanisms; M, Cell wall/membrane/envelope biogenesis; N, Cell motility; Z, Cytoskeleton; W, Extracellular structures; U, Intracellular trafficking, secretion, and vesicular transport; O, Posttranslational modification, protein turnover, chaperones; C, Energy production and conversion; G, Carbohydrate transport and metabolism; E, Amino acid transport and metabolism; F Nucleotide transport and metabolism; H, Coenzyme transport and metabolism; I, Lipid transport and metabolism; P, Inorganic ion transport and metabolism; Q, Secondary metabolites biosynthesis, transport and catabolism; R, General function prediction only; S Function unknown.</p

Number of ESTs falling into different GC content ranges among a total of 403 ESTs that had a hit against the <i>P. infestans</i> genes.

<p>Number of ESTs falling into different GC content ranges among a total of 403 ESTs that had a hit against the <i>P. infestans</i> genes.</p

Main workflow of analysis followed in this study.

<p>Main workflow of analysis followed in this study.</p

GenBank accession numbers and descriptions of the sequences used for this study.

<p>GenBank accession numbers and descriptions of the sequences used for this study.</p

Distribution of ESTs within contigs after clustering (using CAP3) the 22,795 sequences downloaded from GenBank.

<p>Distribution of ESTs within contigs after clustering (using CAP3) the 22,795 sequences downloaded from GenBank.</p

Different criteria used to separate the <i>P. infestans</i> sequences from host sequences produces results that differ notably among them.

<p>12,900 unitigs containing host and pathogen sequences were used to test different approaches to separate both types of sequences. The scheme represents the number of sequences obtained using GC content and a BLAST cut-off e-value combined with different ratio cut-offs: ((Alignment length * %ID)/Unitig length). (a) GC >52%; (b) e-value cut-off of 10⁻¹⁵ (c) e-value cut-off of 10^-15and ratio >50%; (d) e-value cut-off of 10⁻¹⁵ and ratio >60%; (e) e-value cut-off of 10⁻¹⁵ and ratio >70%; (f) e-value cut-off of 10⁻¹⁵ and ratio >80%; (g) e-value cut-off of 10⁻¹⁵ and ratio >90%.</p

Summary of resulting candidate <i>Phytophthora infestans</i> sequences after separating 12,900 unitigs containing pathogen and host sequences using different selection criteria.

<p>The sequences identified as belonging to <i>P. infestans</i> but also having a hit against potato and tomato ESTs or any Solanaceae are shown to the right.</p>a<p>((Alignment length * %ID)/Unitig length).</p