filter_transcripts

python script for filtering initial transcriptome assembl

Comparison of the general performance of the three approaches and expected values.

<p>Comparison of the general performance of the three approaches and expected values.</p

Rubens_transcriptome_annotated

Output of transcriptome annotation from Blast2G

Diagram depicting the three alternative multigene family amplification strategies compared in this study.

<p>When amplifying multigene families, or other complex targets, some alleles may contain variants in the priming region, here reflected by colored bars. (a) Primer design: The conventional strategy tries to match all known variation by designing highly degenerate primers, but some variants might be missed because of unknown variation or in an attempt to avoid highly-degenerate primers. Degenerate nucleotides in the primers are represented by bars with more than one color. In the pooled-PCRs strategy, allele groups with similar priming regions are targeted separately with low-degeneracy primers and by taking into account the observed phase. In the pooled-primer approach, non-degenerate primers targeting each known flanking region are pooled according to the expected number of targeted alleles. (b) PCR amplification: The conventional and pooled-primers strategies amplify all alleles in a single PCR while in the pooled-PCRs strategy an independent PCR is performed for each primer pair. Both the conventional and pooled-PCRs approaches yield unbalanced libraries, but in the case of pooled-PCRs each library is biased toward a different set of alleles. Biases in the pooled-primers approach are minimized because all alleles are primed by perfectly matching primers at the right concentration. (c) PCR yield pooling: This step is exclusive to the pooled-PCRs approach and attempts to produce a final balanced sequencing library by pooling independent PCRs taking into account the number of perfectly targeted alleles. Note that this diagram is a sketch for illustrative purposes only and does not reflect the alleles, primers or libraries used in this study.</p

The relationship between general intelligence faktor g, broad cognitive abilities and working memory

This thesis deals with the relationship between Working Memory, Working Memory Span tasks and general factor g and Broad cognitive abilities. Measured constructs are introduced in the theoretical part, with their evolution, various methods of their measurement and studies investigating the relation between them. The empirical part of the research has been conducted to verify the relationship between Working Memory and general intelligence factor g. It has been done to reveal the relationship between Working Memory Span tasks and Broad cognitive abilities as well. The question concerning the influence of the use of strategy while performing the automatic version of Working Memory Span tasks has been investigated as well

Relationships between average allele coverage, probability of detection, and the number of matching PCRs.

<p>Relationships between average allele coverage, probability of detection, and the number of matching PCRs.</p

Standardized amplification efficiencies for each allele obtained with the three amplification strategies.

<p>For easier comparison alleles are ranked from one (the lowest) to 13 (the highest) within each strategy, and thus numbers do not identify specific alleles. The range of standardized amplification efficiencies is approximately two times and four times larger using the conventional strategy than the pooled-PCRs and pooled-primers approaches, respectively.</p

Allelic profile completeness obtained with increasing coverage.

<p>The same set of individuals was assayed with the three strategies and the reads obtained for each amplicon were bootstrapped to simulate lower coverages (increasing steps of 10 reads, 100 iterations). Profile completeness is defined as the proportion of the alleles in the individual’s inferred profile (from the pooling of all available data) that were scored in each iteration. Both the average value and its confidence interval (95%) are represented. Note that increasing the coverage does not compensate for highly biased amplification efficiencies (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0157402#pone.0157402.s002" target="_blank">S2 Fig</a> for larger sampling sizes).</p

Heatmap of the 5,150 differentially expressed transcripts.

<p>FPKM values have been log transformed and scaled. Color intensity indicates expression level. Similarity between stages with hierarchical clustering is shown above the heatmap.</p

Life cycle of <i>Chorthippus biguttulus</i> indicating developmental stages and seasonal timing.

<p>Life cycle of <i>Chorthippus biguttulus</i> indicating developmental stages and seasonal timing.</p