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Annotate gene?

Posted: Thu Apr 24, 2014 8:46 pm
by drevie
One contig has an exon with a match to the beginning of a RNA directed DNA polymerase of D. melanogaster (e 10-45). The gene is normally found in a retrotransposon transposable element, but RepeatMasker doesn't show it as a repeat. Is this because the repeats of D. biarmipes are enough different? Should they annotate it?

Re: Annotate gene?

Posted: Thu Apr 24, 2014 10:47 pm
by wleung
Please add a note in the "Preparing the project for submission" section of the GEP Annotation Report indicating that the gene prediction most likely corresponds to a unmasked transposon fragment.

The species-specific transposon library used by RepeatMasker is constructed by comparing the entire genome assembly against itself and then looks for regions of the genome with multiple alignments. Because of the limited amount of paired end 454 reads and the short read length of the Illumina reads, many repeats in the D., biarmipes assembly could have been misassembled. This would affect the quality of the repeat library and lead to an underestimate of the true repeat content of the D. biarmipes genome. Hence RepeatMasker will likely miss some of the transposon fragments in the D. biarmipes contig.