Sequencing reads were aligned on the human reference genome build 37 (GRCh37) and human reference mtDNA sequence (revised Cambridge reference sequence, rCRS [ Andrews et al., 1999]), mainly by BWA alignment tool.
To be able to compare hominid mtDNA sequences to each other, as well as, to 4902 human database sequences, all sequences were aligned to the human reference sequence (revised Cambridge Reference Sequence, rCRS, NC_012920 [ 18]) with the ClustalX 2 software [ 39].
In order to be able to perform site-by-site comparisons with the 4902 Homo sapiens sequences that were available at the GenBank database at the date of this study, we aligned all sequences to the human mtDNA reference sequence (revised Cambridge Reference Sequence, rCRS [ 18]), and annotated polymorphic positions according to the rCRS numbering.
Moreover, inspired by our cartoon model of temporal-spatial sequences (revised Figure 7), they are asking whether the early and late spatial templates display different spatial-temporal correlation values with the temporal sequences during the preceding sleep.
JB has carried out the main genome comparisons, designed and executed all experiments, participated in the gap closure of the genome sequence and revised the sequence.
In this report, we characterize these four T. vaginalis Mutator-like elements (TvMULEs), which we renamed as TvMULE1 (based on the R210 sequence), TvMULE2 (based on the R130a sequence, here revised regarding to sequence and structure), TvMULE3 (based on R119) and TvMULE4 (based on R165).
TS carried out the searching of the literature, drafted the results tables and manuscripts; MP developed the design of the study and a conception for data interpretation; improved the draft; IG participated in the sequence alignment, revised the paper; WG participated in the sequence alignment; revised the paper.
LCT had participated in the sequence alignment, revised the manuscript.
During summer 2003, with a grant from the Faculty Science Council and College Center for Science Education, the sequence was revised to include a MATLAB (The MathWorks, Natick, MA) component.
Although our laboratory had previously completed the total synthesis of haouamine A (2), the synthetic route was not amenable to large-scale synthesis, and therefore, prompted by Rami Hannoush at Genentech, the sequence was revised.
The latter type of change is reflected only by a change to the modification date of the record, and will be changed if the gene symbol changes, citations associated with the record change, or the position of features (such as the coordinates of exons) within that sequence are revised.
