Recent advances in SNP detection and the availability of large genomic sequence datasets from diverse accessions allows trait variation to be dissected by genome wide association studies (GWAS), which offers a much higher mapping resolution compared to the RILs [ 28, 36– 36].
We have found that 299 (70%) of the 427 S. mansoni genes (Additional file 2) are not present in the S. mediterranea EST [ 12] and genomic sequence datasets.
We used the BLASTX algorithm [ 36] to identify ESTs with sequence similarity to the protein sequences derived from the genomic sequence datasets of 15 eukaryotic species (two animals, two plants and eleven fungi).
To further delineate the extent of conservation and estimate the time of acquisition of this element in evolution, we searched available genomic sequence datasets or performed PCR analysis on the intergenic junction region between the TIGD1 and EIF4E2 genes in a panel of primate and other mammalian genomic DNAs.
Our analyses of the first large-scale genomic sequence datasets from copepod germline and soma show that the vast majority of the excised sequences are non-simple, non-tandem (within the length of a single read) repeats of known TE or likely TE origin.
Hydra-Multi was originally developed to explore the mechanisms driving complex genomic rearrangements among 129 whole genome sequencing datasets (64 tumors and 65 matched normal tissues, Supplementary Table S1) from TCGA (Malhotra et al., 2013).
The bank package provides operations related to standard genomic sequence dataset management.
The resulting non-redundant genomic sequence dataset consisted of ~45,000 sequences, of which ~29% were putative coding sequences and ~70% were in common between the mapping parents.
For example, we applied GeneSV to estimate frequencies of mutations observed in codon positions within different genes within the set of all available genomic sequences (dataset 2013.02.18).
The 454 pyrosequencing-generated genomic sequence dataset consisted of 570912 reads, with the average read length at 262 bp, totaling 150 Mb (Short read archive SRA008127).
