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The largest variation is expected to be between sequences from different classes.
Dinucleotide composition is highly stable within a genome and can distinguish between sequences from different species.
Again, orthologous introns with significant similarity (bl2seq E-value ≤ 0.0001) between sequences from different pairs were excluded from analysis.
Sets of orthologous introns with significant similarity (bl2seq E-value ≤ 0.0001) between sequences from different pairs were excluded from analysis.
The divergence between the variants within an individual was always less than the divergence between sequences from different species (Table 2).
A pairwise protein-protein sequence comparison was first performed on these selected SGPs using "BLAST 2 Sequences" [ 63] to find regions of local similarity between sequences from different Anopheles taxa.
Similar(49)
InParanoid detects mutual best hits between sequences from two different species.
Inparanoid [ 17] is based on pairwise similarity scores and it detects best-best hits between sequences from two different species to form the main orthologous group to which other sequences (in-paralogs) are added only if they are closely related.
However, we found only one true recombinant in our dataset and no evidence of past recombination events in the comparison between sequences from two different species (within the hybrid).
The surrounding panels show fragments of the alignment between TfR1 sequences from different species (human, mouse, rat, hamster, cat and dog).
As with the "all scaffolds" approach above, the BLASTN output was parsed to find all instances of overlap >1,000 bp in length with >90% identity between cDNA sequences from different metagenomes.
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