Most of the existing plant genome browsers provide conventional data on gene models, transcripts, duplication, syntenic regions and repetitive elements.
We find that the majority of transcripts of duplication peptides have exons that align to a single unique macaque alignment net (66%).
As regards Ciona intestinalis, in the assembly v2.0 the sequence of chromosome 5 matching the experimental htt transcript shows duplications and transpositions of some regions, whereas in the assembly v1.95 almost the entire htt transcript matches consistently the sequence of a single scaffold.
We explore the abilities to examine differential expression, gene duplication, transcript assembly, alternative splicing and SNP discovery.
This is a complex task, due to presence of alternatively spliced transcript variants, gene duplications, allelic polymorphisms and noise due to suboptimal sequence quality, which often leads to the generation of a high number of short and poorly assembled contigs [ 55].
The GS de novo (NEWBLER, Roche/454 Life Sciences) assembly program is set up to allow for improved contig alignments when there is abundant alternatively spliced transcripts and gene duplication events by allowing reads to be split into two and each portion assigned to a different contig.
Instead, biological factors involving gene duplication or transcript processing may complicate the unambiguous assignment of signatures to transcripts.
We defined a pseudogene as a duplicated transcript that has lost its original function due to incomplete duplication or at least one interruption of the ORF.
Filamin C (FLNC) appears to be a true duplication, with transcripts divergent at the nucleotide and protein levels.
Trinity has been found to efficiently reconstruct the transcriptome, inclusive of the splicing events and transcripts resulting from recent duplication events, better than other available de novo transcriptome assemblers [ 26].
The presence of a predicted 'Cldn4-like' sequence in rat (between Cldn4 and the degenerative Cldn13-like sequence on rat chromosome 12) but with no transcript evidence, suggests a gene duplication prior to mouse/rat speciation events.
