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The initial alignment is stored in the first section.
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The results of the clustering by alignment were stored in a relational database.
The information gathered in these alignments is stored in the database.
The raw RNA-Seq reads between treatment and control conditions are aligned to the reference genome sequences by TopHat2 [ 15], and the resulting alignments are stored and sorted in BAM files, defined by [ 16].
Player alignments were stored in CIGAR format (Li et al., 2009) with associated alignment start position.
Trees and alignments are stored in the database phylomeDB with the PhyID code 178.
The alignments were stored in both PSICOV (Jones et al., 2012) native and A3M formats.
E-values, bit scores and local alignments are stored in the 'Similarity Data' table for all significant matches.
Finally, all results of the RNAz screen and the corresponding alignments were stored in a relational database for further processing and analysis of the structured RNAs.
All hits with e-value less than 0.001 and their associated alignments are stored in the database and tracked with any associated functional annotation.
Resulting trees and alignments are stored in phylomeDB [ 26] (http://phylomedb.org), with the phylome IDs 150 (P. digitatum) and 179 (P. chrysogenum).
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