Today Ball State, located in Muncie, has a Center for Middletown Studies, which collaborated on the reading database.
For the taint marked data, the behavior of the reading database will be processed.
YR provided read wrangling support by collecting sequence data and building the reads database prior to assembly.
The sequence reads were submitted to the Sequence Read Database (http://www.ncbi.nlm.nih.gov/sra) and the SRA study accession for the M. paratuberculosis 43525 genome sequence is SRP033522.
Transcriptome sequences were deposited into the short read database of the National Center for Biotechnology Information (NCBI) [accession number SRP009188].
Focusing on the most abundant CarSat1 family, we divided the CarSat1 read database into those that contain CENP-A-associated k-mers (CENP-A) and those that lack entirely any association with CENP-A (CENP-A).
It is notable, however, that we find overlap with sites of conserved sequence elements identified within the centromeric read database.
K-mers not specific to the centromeric database, as demonstrated by an exact match to reads outside of the defined read database, were eliminated.
Alfalfa transcriptome sequences were submitted to the short read database and transcript assembly database in GenBank (http://www.ncbi.nlm.nih.gov) and were assigned the accession numbers [Genbank: JL866457- JL881209], [Genebank: JL881210- JL898333], [Genbank: SRX040822], and [GenBank: SRX040823], respectively for Wisfal short reads, Chilean short reads, Chilean assembly, and Wisfal assembly.
To explore sequence variation within the centromeric read database and as a prerequisite for searching for specific sequence features that distinguish functional centromeres from related (but non-functional) sequences, we reformatted the entire canine unmapped database and the remaining unassigned "gap" reads into a library of k-mers (see Methods).
