"... In PAGE 11: ... Since the dataset we used to test the programs was composed of 103 human and 92 murine (82 Mus musculus and 10 Rattus norvegi- cus) sequences, we wanted to investigate whether such a phylogenetic mix can corrupt the performance of the gene-finding programs, especially those calibrated for human sequences. The AC values on the nucleotide level and for (ESn + ESp)/2 on the exon level for each of the pro- grams, but separately for human and murine se- quences, are given in Table7 . It can be observed that the difference in accuracy measures between human and mouse/rat are marginal.... ..."

"... In PAGE 2: ... Answering these questions will facilitate iden- tification of primitive (general) and derived (specialized) aspects of Runx gene structure, function and regulation. Results and discussion The collection of Runx gene sequences from phylogeneti- cally diverse model organisms Sequence similarity searches of public databases using the BLAST program [6] were used to collect a set of currently available Runx gene sequences (listed in Supplemental Table1 ) from phylogenetically diverse species with com- plete or nearly complete genome sequences. Previously undescribed Runx genes collected in our BLAST searches include two genes from the puffer fish (Takifugu rubripes) genome, a single gene from the sea squirt (Cionia intestina- lis) genome, three genes from the mosquito (Anopheles gambiae) genome, and two new Runx genes from the fruit fly (Drosophila melanogaster)genome.... In PAGE 4: ... The arrow indicates a highly conserved intron that falls within sequence that encodes the purine nucleotide-binding consensus. Note that the Runt domains from the spider gene Cs2 and the nematode gene Mh are partial, as indicated by the x apos;s; these partial sequences were not used in the alignment used to generate trees ( Table1 and Figure 3). Abbreviations are as in Figure 1, with the addition of Pl, Pacifastacus leniusculus; Cs1, Cupi- ennius salei Run-1, etc.... In PAGE 5: ...tode (M. hapla). The consensus topology produced by each method was largely consistent with accepted phylog- enies for all nodes with significant bootstrap values (Fig. 3); the main observations derived from each method are summarized in Table1 . The consensus of phylogenetic approaches strongly indicates the monophyly of the deu- terostome Runx genes in the collection, with the expected relationships (echinoderms(urochordates(vertebrates))).... In PAGE 5: ... 3 and Table 1), arguing against an earlier proposal for the basal posi- tion of Runx3 [8,13] among the vertebrate genes, which was inferred from relative gene size, exon-intron structure, and pattern of expression. While the consensus of trees summarized in Table1 is for the most part consistent with the expected monophyly of the protostome genes in our collection (nematodes, ar- thropods), the branching order is ambiguous. Among the as was also suggested by intron positions (Fig.... In PAGE 7: ... Methods Collection and assembly of previously uncharacterised runx genes quot;seed quot; sequence was found in C. intestinalis gDNA, Ti 119616831 (Supplemental Table1 ), by a MegaBLAST search using nucleotide sequence encoding exon 3 of SpRunt in the NCBI Trace server site http://www.nc- bi.... In PAGE 8: ...rom similarities to MmRunx2 and Danio rerio runtb, respectively. TrRunx2 was recently published [11]. M. musculus distal tran- scripts were gathered from Genebank entries and verified with publications (see Supplemental Table1 ). Note: Unlike all of the other vertebrate Runx genes in our collection, TrRunx1 transcript from P2 has a small exon (encoding 9 amino acids) followed by a 1 kb intron (see also B, below, and 3).... In PAGE 9: ... purpuratus Runt protein sequence as the query. The newly identified Drosophila Runx gene sequences (CG1379 and CG15455) are present in a single sequence file (see Supplemental Table1 ) and with opposite coding orientation and were named for this study RunxA (CG1379) and RunxB (CG15455). No cDNAs specific for the mosquito Runx genes or for the Drosophila RunxA or RunxB genes was found despite an extensive search, so pu- tative intron positions were manually located in these genes by spliced alignment as described above.... In PAGE 9: ... rerio) were used to place the start of the cod- ing region in the distal promoter of TrRunx1 and TrRunx3, and cDNA sequences from the teleost O. laptipes were used to place the start of the coding region in the distal promot- er of TrRunx2 (Supplemental Table1 ). The promoter structure of TrRunx2 published by Eggers et al.... ..."

"... In PAGE 10: ...lasma species discussed above (i.e., a lower E-value implies a closer phylogenetic relationship). Table4 shows the high-scoring Motile Group Phylogenetic Bias genes. Several interesting candi- dates are identified by this method.... In PAGE 13: ...road Institute (Galagan et al. 2002, 2003). GLIMMER (Delcher et al. 1999) was run on the whole genome using protein translation Table4 to generate an initial set of ORFs. GLIMMER ORFs longer than 200 bp were annotated as genes if they did not overlap with an adjacent ORF by more than 30 bp.... ..."

"... In PAGE 9: ... The genes are in descend- ing order according to their DP scores (see Methods for an explanation of this derivation). In this way, genes present at the top of each group in Table5 are the most important to differentiate and define each branch of genomes in the tree. The profiles column marks with a 1 the presence of a certain gene in a specific genome.... In PAGE 9: ... Each number (1 or 0) corresponds to 1 of the 20 species ordered from left to right as enumerated in Table 4, starting with Synechocystis. Table5 shows 12 genes that are most specific to Cyano- phora cpDNA and only common with Synechocystis: clpP, crtE, groES, hemA, mntA, mntB, nadA, and 5 hypothetical proteins. These genes could be considered as coding for the most con- served genes from the ancient chloroplast, among those that show variation.... In PAGE 13: ...Table5 ) were identified in the case of land plant chloroplast genomes: maturase (matK), NADH dehydrogenase (ndhA, B, C, D, E, F, G, H, I, J, and K), one subunit of cytochrome b6/f (petL), and another subunit from photoystem II (psbM). The presence of maturase is a distinct feature in higher land plants directly related with the appearance of introns (see Table 1; Wolfe et al.... In PAGE 14: ... gracilis and E. virginiana cpDNAs are also included in Table5 . For Euglena not much can be said because all correspond to hypothetical proteins.... ..."

"... In PAGE 9: ... In Blochmannia, polyketides can furthermore be involved supporting the lipid metabolism in the host, in particular regarding insect hormones. The phylogenetic distribution of the previously con- served hypothetical proteins is shown in Table1 . Interest- ingly, there are no Blochmannia specific proteins among them, even the protein Bfl390 is found in Buchnera and Wigglesworthia.... ..."

"... In PAGE 7: ... The report by the Tele- communications Technology Council (2000) of Japan, listed three types of effects caused by electro- magnetic fields: thermal, stimulation, and other. Table1 explains the relationship between electromag- netic waves and recorded physiological effects (Telecommunications Technology Counc il, 2000, p.33).... ..."

"... In PAGE 13: ... In the end, differences of opinion on particular questions were actually few and judgments were seldom far apart (if anything, there was more disagreement about facts than about judgments). Annex Table2 lists the number of respondents and the ratios of various financial assets and liabilities to GDP. This suggests that at best these indicators could be used across transition economies.... In PAGE 21: ... The five questions which are significant (some, however, at lower t-statistics levels) for both the best and the worst segments are then kept. Table2 provides the results for the group of transition economies and comparator countries combined. Table 2: Relationship of Specific Policies with Quality of Banks... In PAGE 31: ...Table2 : Number of Responses and Differences of Opinion Country Number of responses Number of Differences of Opinion Albania 3 10 Argentina 2 6 Armenia 2 4 Belarus 2 15 Bulgaria I China 3 8 Croatia 2 14 Czech Republic I Denmark 1 Estonia 2 14 Georgia I Greece 1 Hungary 3 6 Kazakstan 2 2 Kyrgyz Republic .3 10 Latvia I Lithuania I FYR Macedonia I Moldova 2 18 Poland 3 8 Romania 1 _ ___ Russia 2 8 Slovak Republic 3 9 Slovenia 2 4 Spain 1 Taj ikistan2 ` 1I Turkey I Ukraine 3 6 Uzbekistan 3 6 Venezuela 1 Vietnam 2 3 Total: 31 Countries 57 151 Notes: In case of three questionnaires, differences of opinion were noted if all three answers were very different (for example, 1, 3 and 5).... ..."

"... In PAGE 5: ..., 2004; Binder et al., in press), the Agaricomycetidae and at least four of the orders within the Agaricomycetidae are probably not monophyletic ( Table1 ). The most problematic order is the Polyporales, which includes representatives of nine different clades.... ..."

"... In PAGE 7: ... Each feedforward controller (FP or FCL) has been designed to perform specifically for its architecture and therefore varies throughout the simulations. Table1 provides a summary of the simulations with a focus on the relationships between certain pairs. We will take a close look at a total of 6 simulations.... In PAGE 9: ... 6.5 Simulation Results This section summarizes the results of each of the simula- tions listed in Table1 . All simulations are run on a block diagram similar to Fig.... ..."

"... In PAGE 18: ... These features that have impact in non functional requirements can be also modeled as software system attributes as shown in figure 1 and related to specific variations such as is mentioned in section 2. Therefore, some Table1... In PAGE 26: ... Both direct and derived relations are sub-classified into other types of relations. Table1 presents a summary and brief explanation of these different types of relations. Note that some types of relations, particularly mutual exclusive and requires, can be both direct and derived relations.... ..."