Because of the jagged start and stop positions and multiple frameshifts and duplications, the standard multiple alignment tools we used failed to give useful alignments of the 454 ultra deep sequence nucleotide data.
Another potentially useful alignment-independent feature is the number of bases that could not be called (N count) in each read.
Most annotated genes that do not form useful alignments are long and repetitive, with the majority being surface antigens.
Because of the high level of divergence between the YLS and M. anisopliae, no useful alignments could be obtained for either orthologous introns or intergenic spacers, and further analysis of deletional biases was not possible.
For example, in the genes with no EST or mRNA alignments, the RNASeq data (14) had no useful alignments to 58%, it confirmed a partial structure in 16%, it confirmed the complete structure in ∼17% and indicated that a structure change was required in ∼9%.
On the other hand, no solution has yet been provided as to how biologists should proceed to select the most useful aligners or alignments.
Manual annotation is well suited to interpreting issues of sequence quality that can compromise the ability of many computational gene builders to utilize ESTs, extracting useful information from them using alignment visualisation tools such as Blixem and Dotter (22, Barson,G. and Griffiths,E., manuscript in preparation).
In the resultant model, the femurs are still in place these will be useful for alignment at a later time.
This additional information may prove useful in alignment.
