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 2: of Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes

Supplementary tables. It includes all supplementary tables. Table S1.List of 114 cancer-related genes. Table S2. Summary of the 33 cancer types. Table S3. Summary of the reported 33 genes involved in 77 events of tumor-specific cleavage patterns. Table S4. Details of all CSs involved in the reported 77 APA events. Table S5. Mapping relations between diseases in TCGA and those in COSMIC (Supplementary Methods). (XLSX 235 kb

Additional file 5: of Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes

Figures available for download. (PDF 86 kb

Additional file 4: of Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes

Supplementary methods. Description of additional methods. (PDF 157 kb

Additional file 3: of Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes

Figure S4. Illustration of all 77 identified events of tumor-specific cleavage patterns. (PDF 5699 kb

Specificity of individual restriction fragments and patterns based on exact and experimental sizing tolerance

<p><b>Copyright information:</b></p><p>Taken from "A BAC clone fingerprinting approach to the detection of human genome rearrangements"</p><p>http://genomebiology.com/2007/8/10/R224</p><p>Genome Biology 2007;8(10):R224-R224.</p><p>Published online 22 Oct 2007</p><p>PMCID:PMC2246298.</p><p></p> dIII restriction fragment specificity for the human genome for fragments within the experimental size range of 500 bp to 30 kb. For a given fragment size, the vertical scale represents the fraction of fragments in the genome that are indistinguishable by size in the case of either exact sizing (fragments in common between two fingerprints must be of identical size) or within experimental tolerance (fragments in common between two fingerprints must be within experimental sizing error; Figure 3) on a fingerprinting gel. When sizing is exact, fragment specificity follows approximately the exponential distribution of fragment sizes and spans a range of 3.5 orders of magnitude. When experimental tolerance is included, the number of distinguishable fragment size bins is reduced and the range of fragment specificity drops to two orders of magnitude. The specificity of a fingerprint pattern of a given size in the human genome. Fingerprint pattern size is measured in terms of number of fragments. Regions with identical patterns are those in which there is a 1:1 mapping within tolerance between all sizeable fragments. The specificity of experimental fingerprint patterns is cumulatively affected by specificity of individual fragments. The specificity of fragments is sufficiently low (that is, due to high experimental precision) so that 96.5% of the genome is uniquely represented by fragment patterns of 8 fragments or more

Detailed reconciliation of sequence and fingerprint alignments for clone 3F05, which contains at least four internal breakpoints

<p><b>Copyright information:</b></p><p>Taken from "A BAC clone fingerprinting approach to the detection of human genome rearrangements"</p><p>http://genomebiology.com/2007/8/10/R224</p><p>Genome Biology 2007;8(10):R224-R224.</p><p>Published online 22 Oct 2007</p><p>PMCID:PMC2246298.</p><p></p> FPP is capable of dissecting complex rearrangements in a clone, as illustrated in this figure showing the internal structure of M0003F05. This BAC was sequenced [26] and found to be composed of content from at least five distinct regions (A-E). FPP detected 4/5 of these regions. BLAT (grey rectangles with alignment orientation arrows) and FPP (thin black lines) alignments of M0003F05 are shown; values underneath coordinate pairs are differences in edge positions between BLAT and FPP alignments

Simulation results of sensitivity and spatial error of rearrangement detection by FPP using experimental sizing tolerance

<p><b>Copyright information:</b></p><p>Taken from "A BAC clone fingerprinting approach to the detection of human genome rearrangements"</p><p>http://genomebiology.com/2007/8/10/R224</p><p>Genome Biology 2007;8(10):R224-R224.</p><p>Published online 22 Oct 2007</p><p>PMCID:PMC2246298.</p><p></p> Sensitivity is measured as the fraction of clone regions of a given size with successful FPP alignments and is plotted for five digests (labeled 1-5). Spatial error is measured by the median distance between FPP and theoretical alignment positions. The largest improvement in both sensitivity and spatial error is realized by migrating FPP from one digest to two. With two fingerprint patterns used to align the clone, 50% of >25 kb clone regions are aligned (90% of >45 kb regions) with a spatial error of 1.7 kb