Our calculations indicate that Alignment B is clearly inferior to Alignment A for both M2 and M1; in fact, the Z values in Table 2 of Alignment B average zero, as expected for an incorrect alignment.
Additional file 10: A table of the alignment positions of flanking sequences of AT rich regions from the F. verticillioides chromosomes to the sequences flanking the centromeres in RRes v4.0 F.
The FlyBase Genes 5.12 with human homologs were selected from hgBlastTab table (identity, length of alignment, eValue) using "Selected fields from primary and related tables" output format.
The Pasteurellacean USS was first characterized in Haemophilus influenzae, whose 1.83-Mb genome contains 1,471 perfect-consensus copies of the 9-bp core of the motif (table 1); alignment of these cores extended the consensus to a 30-bp three-part motif (Smith et al. 1995).
This uncertainty is illustrated by the fact that the topology distribution under the traditional model varies significantly depending on the choice of alignment (Table 1).
Tables of genomic alignments provided by UCSC [ 8] are directly imported to the GeneSeer database.
In addition, 33 complete and 9 near-complete VP1 gene sequences of HEV71 strains retrieved from GenBank and used in this study are listed in Appendix Table 2. Alignment of the VP1 and VP4 gene sequences was undertaken by using the ClustalW program (25 ).
Their sequence ID in this study (see also Additional files 2, 7, 8) and the accession numbers in the database are listed in Table 2. Alignment of the nucleotide sequences was conducted using the Clustal W software [ 44] and was adjusted manually.
After removing low-quality reads, a total of 150 million high-quality clean reads remained, of which 90.48 92.15% were aligned to the reference genome using TopHat (Table 1).> -wrap-foot> Percentage of alignment = high quality reads aligned to genome/high-quality reads.
Using the alignment partners of all housekeeping genes in the yeast interactome, we construct an alignment consistency table of size 1,540×79, which summarizes the network alignments over the shared subsection of tissue-specific networks.
