Figure 7.

Ortholog hit ratio analysis of assembled reads and singletons in the P. hawaiensis transcriptome. As described in [39] an ortholog hit ratio of one suggests that a transcript has been assembled to its true full length. Ortholog hit ratios for two arthropod genomic datasets were obtained by using BLAST to compare the complete Daphnia pulex gene prediction set (downloaded from ftp://iubio.bio.indiana.edu/daphnia/genome/Daphnia_pulex/dpulex_jgi060905/fasta/dpulex-gnomon-transcript-jgi060905.fasta.gz webcite.) with the predicted gene set of Drosophila melanogaster (r5.28 downloaded from ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/ webcite) with an E-value cut-off of 1e-10. (A) Ortholog hit ratio analysis for isotigs. A majority appear to contain at least 50% of the full length transcript sequence (arrow) compared to D. pulex sequences (red), while over one third appear to represent at least 80% of the full length transcript sequence (arrowhead) compared to D. pulex sequences. Comparison with D. melanogaster transcripts (pink) yields comparable ortholog hit ratios. (B) Ortholog hit ratio analysis for singletons. Most singletons produced by both assemblers represent ≤ 20% of full-length transcripts. Arrow and arrowhead indicate 50% and 80% of full-length transcripts, represented by an average of 7.7% and 1.3% of singletons, respectively. In both panels, grey indicates comparison of D. pulex versus D. melanogaster transcripts based on predictions from genomic data.

Zeng et al. BMC Genomics 2011 12:581   doi:10.1186/1471-2164-12-581
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