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All alignments were further aligned to resequencing data from P. taeda (unpublished data) using the profile-profile option in MUSCLE[ 59, 60].
They are further aligned to rule out effects of delay and jitter (variable delay).
The remaining non-annotated scaffolds were further aligned to the nr database.
Unmatched reads were further aligned to primary miRNA sequences and perfect matches registered.
The remaining 18 million unmapped reads were further aligned to exon-intron junctions to identify potential intron retention events.
The remaining 55 (AL) and 58 (AZ) transcripts that could not be mapped to cDNAs from zebra finch were further aligned to the zebra finch genomic sequence.
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On average, 4,479,044 reads per lane failed to align, while a further 4,325,899 aligned to multiple genomic locations.
Introns found in mouse were further globally aligned to human retained intron sequences with needle [ 41] using default parameters and had their percent identities averaged.
We prepared a multiple alignment of the core conserved domain of the TV-Pol family using the KALIGN program, and further aligned them to superfamily A polymerases, including structurally characterized DNA PolIs and the T7 RNA polymerase (Fig. 2).
A further 112 reads aligned to 660 nucleotides of intron 13, generating an alternative N-terminus and premature stop codon (Fig. 11).
From cleaned sequences, we further removed sRNAs aligned to the non-coding RNAs (ncRNA) such as rRNAs, tRNAs, snRNAs and snoRNAs.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com