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However, some gene models from the Phatr2 have to be corrected.
Furthermore, even at 100% sequence identity, some gene models were assigned to other chromosomes.
Some gene models were refined using EST data (Additional file 2).
Some gene models are annotated with the same symbol due to shared homology.
Since this format is highly flexible in production it can easily be updated if future annotations should modify some gene models.
The inferred X. hellerii transcriptome also covers 99%% of gene number and 99%% of nucleotides of the reference X. maculatus transcriptome.> There are several reasons why the RATT tool fails to transfer some gene models to new genomes.
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In some cases, gene models can be quite complex and may have very many transcripts.
The set of non-annotated sequences is likely to include novel 'sponge-specific' genes, although some erroneous gene models may also be present [ 23].
However, despite the usefulness, these databases have performed systematic annotations resulting in different numbers of soybean WRKY transcription factors and some incorrect gene models.
Although our analyses did identify some false gene models, this was balanced by the identification of genes previously missed during the genome annotation, including some that expand the metabolic capacities of T. hominis in interesting ways.
Also, some predicted gene models (TNXB for example) straddle the gaps and almost certainly merge parts of separate loci (TNXA and TNXB for example) that are not completely presented on the assembly because of mis-assembly and/or assembly gaps.
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