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Transcriptome reconstruction was performed using uniquely mapped reads or, alternatively, all the reads (unique and repeated) in order to improve the identification of the transcripts that are duplicated in the P. profundum genome like for example the CRISP elements and to better define the transcript structure of the genes having repeated regions.
In other words, a node is either unique or repeated r times, but it should not be a mixture of unique and repeated k-mers.
The CompareSequences program scans a group of files containing all unsorted FRT-like sequences (both unique and repeated) for the FRT-like sequences homologous to an FRT-like site of interest.
To locate homologous FRT-like sequences, we developed an additional program called CompareSequences that scans all identified FRT-like sequences (unique and repeated) against an FRT-like site of interest and reports sequences that have their level of homology above a set value (Text S10).
Herein, we report novel methods for SNPs calling within unique and repeated genomic regions.
A high coverage depth is essential for the accurate prediction of unique and repeated l-mers in the preprocessing phase of our algorithm.
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Vermeij [ 20] adopted a different approach and examined incidences of putatively unique adaptations and repeated evolution of the same adaptation ("convergent" evolution; Table 1) over the entire history of life.
As an additional validation analysis, we excluded the 112 candidate genes proposed by Barthold et al. (2008) [ 7] from the overall candidate genes list (consisting of 179 unique human genes) and repeated the pathway analysis.
We make use of unique motifs and repeat sequence structure present in KRTAP subfamilies along with phylogeny and blast results to further help identify and classify partial and pseudogenes to the respective subfamilies.
Higher eukaryote genomes are composed of unique and repeat sequences with different biological significances.
In Fig. 2Ci, unique plus repeat sequences have been analysed on one DegTri; using the same map, unique and repeat sequences are separately marked (Fig. 2Cii and iii).
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