"... In PAGE 5: ... First, we eliminated codon usage bias by randomly choosing synonymous codons from the genetic code table. This significantly decreased base pairing for C and G at the third codon sites (Figure 2 and Table 1), pattern of base pairing relative to codon sites (Figure 4 and Table 1) and markedly reduced free Gibbs energy of secondary structure formation at all codon sites ( Table2 ). Shuffling of nucleotides at the third synonymous codon sites which retained nucleotide composi- tion and amino acid sequence of the native mRNAs affected nucleotide base pairing to some extend due to changes in codon context (Table 1).... In PAGE 6: ... mRNA secondary structure and transcript abundance To study the relationship between mRNA secondary structure and transcript abundance, we calculated mRNA folding, codon frequencies and dinucleotide frequencies for different subsets of the human mRNA dataset. The average DG of dinucleotide interaction was significantly lower for abundant messages ( Table2 ). We found no major difference in the pattern and frequencies of base paired nucleotides between the groups of abundant and rare transcripts, and between the groups of long and short transcripts (data not shown).... ..."

"... In PAGE 16: ... The number of genes and other markers associated or linked with human obesity phenotypes continues to expand. The progress made over the last decade is exemplified in the numbers collated in Table8 . The human obesity gene map has become significantly more detailed and complex since the first version developed in 1994.... ..."

"... In PAGE 5: ... Thus, our results represent an addi- tional approach for the understanding of evolution at the genomic level and may contribute to the proper assessment of the evolutionary relationships between extant species. METHODS The rationale for the construction of genomic trees is based on the systematic comparison of the predicted translation products of all surveyed organisms (data taken from original publications; see Table1 ) as a means to determine the pres- ence or absence of genes of common ancestry with an inter- nally calculated threshold of significance. For each organism included in the analysis, every gene product is successively used as a query sequence against all the gene products of the same organism, and against all the gene products of each of Figure 2 Genomic tree.... In PAGE 6: ...i.e., the set is minimal). Note that an ORF product that has no significant match in its own organism ful- fills these properties and therefore is consid- ered as a single member partition. Thus, a partition includes all ORF products with common ancestry in a given organism (the number of distinct partitions are shown in Table1 ). Note that such construction of par- titions is sometimes referred to as the single- linkage clustering method.... In PAGE 6: ... The M. muscu- lus (Mmuniq) and human (Hsuniq) data- bases (see Table1 ) serve solely as targets for comparison by queries of other genomes, with the TBLASTN (Altschul et al. 1990) pro- gram.... In PAGE 6: ... 1. Human and mouse, for which no accurate ancestral gene duplications can be presently calculated, were not considered in this analysis (abbreviations are as in Table1 ). (b) Genomic tree for the considered organisms (minus human and mouse) as obtained from the whole factorial space resulting from the corresponding analysis (see Fig.... ..."

"... In PAGE 6: ... Filling gaps and resolving uncertainties would add additional costs to whole-genome shotgun sequencing in the next century. We assert that the goals listed in Table1 are the true motivation for sequencing the human genome, not the accomplishment of some arbitrary, mythi- cal goal of 99.99% accuracy of a single, artifactual (in places) and nonrepresentative copy of the ge- nome.... ..."

"... In PAGE 9: ...f short repeat unit length (Subramanian et al., 2003). Using TRbase to detect tandem repeats associated with disease genes A key aim of TRbase was to facilitate searches for tandem repeats associated with disease genes. Table2 shows data from a high-stringency TRbase search for trinucleotide repeats in exons of disease genes. Trinucleotide repeat expansions have been shown to cause several human diseases therefore it is of considerable interest to identify such repeats in disease genes.... In PAGE 9: ... Trinucleotide repeat expansions have been shown to cause several human diseases therefore it is of considerable interest to identify such repeats in disease genes. From Table2 it can be seen that the known exonic disease-causing triplet repeats have been identified in the genes CACNA1A (migraine), SCA1 (spinocerebellar ataxia 1), TBP (spinocerebellar ataxia 17) and HD (Huntington apos;s disease). In addition, this search reveals a further 90 trinucleotide repeats in exons of disease genes, including 33 repeats with percentage match scores of at least 90% (Table 2).... In PAGE 9: ... From Table 2 it can be seen that the known exonic disease-causing triplet repeats have been identified in the genes CACNA1A (migraine), SCA1 (spinocerebellar ataxia 1), TBP (spinocerebellar ataxia 17) and HD (Huntington apos;s disease). In addition, this search reveals a further 90 trinucleotide repeats in exons of disease genes, including 33 repeats with percentage match scores of at least 90% ( Table2 ). Therefore TRbase is a useful tool for identifying both perfect and imperfect tandem repeats associated with disease genes, further study of which may be informative about the genetic basis of disease.... In PAGE 9: ... For example, Table 2 shows that the RUNX2 gene contains 22 copies of a CAG repeat. Like the known disease- causing triplet repeats shown in bold in Table2 , this encodes a polyglutamine tract and is subject to length polymorphisms (Vaughan et al., 2002).... In PAGE 9: ... (2002) concluded from a study of 495 Australian women that they may be correlated with reduced bone mineral density and bone fracture. Table2 also shows that RUNX2 contains a second, shorter trinucleotide repeat, which encodes Figure 2 Approx. ... In PAGE 10: ..., 2002). As a further example, Table2 shows that the HD gene contains two trinucleotide repeat sequences: the CAG repeat known to be associated with Huntington apos;s Disease and an adjacent CCG triplet repeat coding for a stretch of proline residues (shown as GCC consensus in Table 2). This CCG triplet repeat has implications for diagnostic testing as it is also known to be polymorphic (Andrew et al.... ..."

"... In PAGE 4: ... We analysed a subset of these mechanisms consisting of four approaches developed in the AWARENESS project (CMF, CCS, CDF, JEXCI)[3], and one approach developed in the AMIGO project (CMS)[7] and four external approaches (Context Toolkit [5], PACE [2], Solar [8], and JCAF[4]). The result of our analysis is presented in Table1 . The analysis consisted of review- ing the following aspects of the different discovery mechanisms: Interaction mechanism: what interaction mechanisms do the analyzed discov- ery mechanisms support? Interaction syntax: what information is expressed in the context discovery re- quest? Interaction format: what is the data format of the request and response? ... ..."

"... In PAGE 1: ... There already exist a number of automated or semi-auto- mated complete genome annotation systems. For example, GeneQuiz [8] and PEDANT [9] are two pipelines that are comprehensive and highly automated ( Table1 ). Similarly, there are several sites that provide protein structure annota- tions for various genomes.... In PAGE 2: ... Results and discussion Automated annotation pipelines are crucial to organize the deluge of genomic information. Table1 compares features of iGAP with those of GeneQuiz and PEDANT, two established genome annotation methodologies. GeneQuiz focuses on homolog and function assignment through sequence similar- ity search; PEDANT is a comprehensive analysis pipeline with emphasis on gene prediction, secondary and tertiary structure assignment; iGAP puts much more emphasis on fold recognition, threading and, to be released in the near future, homology modeling.... In PAGE 8: ...re included. The non-NR entries (contributed by Ceres, Inc) were absent from NR of NCBI at the time of analysis. 1gp4, 1gp6, and 1e6b were not in SCOP release 1.55 or the FOLDLIB in this study (see Table1 b). 1j6y was an NMR structure and was excluded.... ..."

"... In PAGE 3: ... cerevisiae codes for proteins. Table1 shows the fraction of coding for each chromosome (about 70%). In higher organisms this quantity drops, down to about 5% in humans (see the gene HUMHBB in the table).... In PAGE 5: ... cerevisiae. The results, given in Table1 , show that this DNA walks have a signi cantly lower dimension than 2D RW. An RW is compact in two di-... ..."