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Such sequences were confirmed as recombinant by inspection or if, when they were divided at the presumed point of recombination and analyzed as separate sequences, one portion was phylogenetically St-like and the other was H-like.
Individual sequences were annotated with cluster membership information and maintained as separate sequences for further annotation.
In addition, individual LHCs from polycistronic [ 63] or polyprotein [ 64, 65] sequences were treated as separate sequences.
First, some contigs are expected to lack matches in public databases and therefore remain as separate sequences after contig-joining.
The distances between nucleotides within each gene were considered as separate sequences and the distance distribution was computed from all the genes.
The second tool both trims and splits the reads by extracting from the corrected reads all runs of solid bases as separate sequences.
Similar(53)
Finally a redundancy criterion is applied to each variable position in the family alignment before a sequence is validated as a separate gene sequence thus reducing the inclusion of sequences differing by random cloning or sequencing errors as separate gene sequences.
For Brachypodium nadpme-I, which is composed of two repeats of the standard coding sequence (fig. 1), each repeat was treated as a separate sequence in phylogenetic analyses.
Drosophila pseudoobscura was chosen because its genome assembly is more than just a WGS assembly, as it is augmented by separate sequences of repeat regions (Richards et al. 2005).
We were able to merge exons from genes that had been previously predicted as separate coding sequences [ 27]; these merges resulted in a more complete or contiguous annotation for 394 genes and their corresponding transcripts (see Additional file 3).
The introns and exons were defined as separate modules (sequence of the flanking BsaI restriction sites shown in Fig. 2, sequence of the complete modules given in Fig. S1).
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