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Another assembling problem is posed by the high sequence similarities among closely related species.
Amplification of specific HIV genome regions is complicated by the high sequence diversity of the HIV genome.
The quality of the modeled structure was ensured by the high sequence identity between AAH and TibC (68%).
All of these unigenes were highly homologous to MXMT, as shown by the high sequence similarity between 7-NMT and MXMT.
For hybrid KIR genes, precise definition of the limits between the regions derived from particular KIR can be restricted by the high sequence similarity of these genes and the limited number of genomic (intron) sequences presently available.
To date, efforts to resolve the deep evolutionary origins of this ancient protein family have been hindered by the high sequence divergence between paralogous groups (i.e. ~30% average pairwise identity).
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This hypothesis is also supported by the high sequencing coverage observed in the highly fragmented and gene-poor fraction of the assemblies (Additional file 6: Figure S2A).
The duplication rate decreased from 52.5% to 37.0% when using the downsampled data and thus the high duplication rate can only be explained partly by the high sequencing depth.
However, some of the chemosensory gene transcripts were not accurately predicted by Cufflinks, probably due the high sequence similarity of tandemly duplicated genes.
Based on the high sequence coverage by trypic fragment analysis, two vitellogenins (VTG1, VTG4) could be identified.
Regulatory sequences beneath Foxa1 peak regions called by MACS were selected according to the limits defined by the highest sequence conservation among multiple vertebrate species from the UCSC genome browser (http://genome.ucsc.edu/).ucsc.edu/
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