AA and JH performed alignments, splice junction detection, gene based analysis and statistical analyses.
After removing sequences that failed alignment and splice site validation criteria (see Methods), 62,275 ESTs that align to bulk (non-rDNA) MAC chromosomes remained.
We mapped the original ESTs on the extracted genomic sequences with SIM4 (A = 4, P = 1) to extract the alignment and splice site information.
In addition, regarding prediction of splice-junction peptides, these data are greatly informed by the use of long reads and paired-end mRNA-seq to enhance alignment across splice junctions.
Only alignments with splice site directionality coherent with the alignment strand of mRNAs in the cDNA cluster were accepted.
Based on whether the aligner support splice reads alignment, we can divide aligner into two categories: unspliced aligner and spliced aligner.
The dimensions of the LMA-10 PCF simplify alignment and splicing with the SMF with a standard splicing machine and minimize the loss due to mode-field diameter mismatch compared to other PCFs.
A companion website provides visualization of the EST alignments and splice graphs for each cluster showing alternative splicing, as well as access to the alignments themselves and additional information (see http://combi.cs.colostate.edu/as/chlamy/).edu/as/chlamy/
Briefly, mRNAs and ESTs were aligned to the genome using SIM4 [ 32] to obtain alignments with splice sites precisely defined.
