BF, together with HD, contributed to the genome search and compiled the sequence alignments.
JFA performed the computational analyses, compiled the sequence databases, processed the MASCOT results, and ran the GO functional and KEGG annotation.
IM and AS compiled the sequence data and performed the computational analyses, IM, EB, YS, NLK, RZ carried out the molecular analyses, IM, AS, EB and TP drafted the manuscript.
Since the automatically performed annotation was not able to correctly predict the protein sequences (the N- and/or C-termini often were missing), it became necessary for comparative analysis to re-compile the sequences on the basis of an exon-intron dataset of known h/E spl) genes.
We used the information obtained from the Pfam database [ 41- 43] and Uniprot [ 44, 45] along with BLAST searches [ 46] of sequenced eukaryotic genomes at the DOE Joint Genome Institute (JGI), the Broad Institute, the J. Craig Venter Institute, ToxoDB [ 47], NCBI, dictyBase [ 48] and the Arabidopsis Information Resource (TAIR) [ 49] to compile the sequences of over 300 PARP proteins.
JYC compiled the RT sequences, participated in software development, and helped with phylogenetic analysis and sequence alignment.
We compiled the homologous sequences of these two genomic regions from 25 vertebrate species for comparative analyses (Table 1).
We compiled the resulting sequences using CodonCode Aligner (CodonCode; Dedham, Massachusetts) [ 14] with default parameters (Version 3.7.1.1), aligning each amplicon to the published reference sequence.
To characterize the repetitive unit, or monomer, I compiled the DNA sequences generating clusters of overrepresented 13-mers (i.e., X/A > 20).
