SPAT: Searching for Poly(A) Tails in RNA-Seq de novo Assemblies

<p>A method for detecting alternative polyadenylation in RNA-Seq libraries using de novo assembly with ABySS. It will be presented at HiTSeq and ISMB 2013 by Anthony Raymond.</p

Additional file 5: Supplementary Figures. of Comprehensive whole genome sequence analyses yields novel genetic and structural insights for Intellectual Disability

Figure S1. IGV image and Sanger verification trace files for indel in ARID1B and missense variation in UPF1. Figure S2. UK10K mutation load – counts as per variant annotation type on one patient. Figure S3. Histogram of mutation burden per patient in the UK10K cohort. Figure S4. Pathway interactions showing convergence onto UPP pathway. Figure S5. Plots for CNV distribution for two chromosomes as called by CNAseq. (DOCX 1972 kb

Additional file 4: Table S3. of Comprehensive whole genome sequence analyses yields novel genetic and structural insights for Intellectual Disability

UK10K study cohorts that comprise the positive control cohort – Table giving descriptions of the study cohorts from the UK10K project that comprised the positive control cohorts and conditions for use. (XLSX 13 kb

Additional file 1: of Comprehensive whole genome sequence analyses yields novel genetic and structural insights for Intellectual Disability

Supplementary Methods - Additional details on methods presented succinctly in main text. (DOCX 53 kb

Distribution of Orthologous CDSs in Y. enterocolitica 8081, Y. pestis CO92, and Y. pseudotuberculosis IP32953

<div><p>The Venn diagram shows the number of genes unique or shared between two other <i>Yersinia</i> species (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020206#s4" target="_blank">Materials and Methods</a>). The associated pie charts show the breakdown of the functional groups assigned for CDSs in relevant sections of the Venn diagram. Colour code for the pie charts is as follows: hypothetical proteins (1); conserved hypothetical proteins (2); chemotaxis and motility (3); chromosomal replication (4); chaperones (5); protective responses (6); transport and binding proteins (7); adaptations to atypical conditions (8); cell division (9); macromolecule degradation (10); synthesis and modification of macromolecules (11); amino acid biosynthesis (12); biosynthesis of cofactors, prosthetic groups, and carriers (13); central intermediary metabolism (14); small-molecule degradation (15); energy metabolism (16); fatty acid biosynthesis (17); nucleosides and nucleotide biosynthesis and metabolism (18); periplasmic/exported/lipoproteins (19); ribosomal proteins (20); laterally acquired (including prophage CDSs) (21); pathogenicity and virulence (22); general regulation (23); and miscellaneous function (24).</p><p><i>Y. en, Y. enterocolitica</i> strain 8081; <i>Y. pstb, Y. pseudotuberculosis</i> strain IP32953; <i>Y. pestis, Y. pestis</i> strain CO92<i>.</i></p></div

Microarray Analysis of the Plasticity Zone of 34 Isolates of Y. enterocolitica Biotypes 1A, 1B, 2, 3, and 4

<p>Microarray analysis of the genomic DNA from 34 Y. enterocolitica isolates, representing five biotypes, constructed using GeneSpring version 6.1 software. Data is presented for the CDS in the range of YE3439–YE3658 including the PZ and YGI-1, as marked (left side). Each numbered column represents the results from a different Y. enterocolitica strain: 1, 09/03; 2, 12/02; 3, 208/02; 4, 35/03; 5, 77/03; 6, 30/02; 7, 81/02; 8, 14/02; 9, 119/02; 10, 212/02; 11, 218/02; 12, 231/02; 13, 56/03; 14, 16/03; 15, 209/02; 16, 149/02; 17, 177/02; 18, 153/02; 19, 202/02; 20, 7/03; 21, 135/02; 22, 8/03; 23, 190/02; 24, 220/02; 25, 227/02; 26, 201/02; 27, Y30; 28, Y73; 29, Y89; 30, Y71; 31, Y68; 32, Y70; 33, Y69; and 34, 8081 (control). See <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020206#pgen-0020206-st002" target="_blank">Table S2</a> for details. The colour-coded biotype key for each isolate is shown at the bottom. Each row represents an individual gene within this region. Coloured blocks (right side) have been used to highlight groups of CDSs showing differing distributions between isolates. The range of CDSs encoded within these blocks is shown (in brackets). Also marked are the relative positions of interesting CDSs or loci that have been mentioned within the body of this article. Blue CDSs correspond to those genes that are considered absent/divergent, and yellow CDSs correspond to genes that are assigned present/conserved. Grey indicates data not obtained.</p