The use of multiple alphabets in kappa-gene immunoglobulin DNA sequence comparisons.

Comparisons within and between the human, mouse and rabbit immunoglobulin-kappa gene (J-C region) DNA sequences are carried out in terms of three two-letter nucleotide alphabets: (i) S-W alphabet (W = A or T; S = G or C); (ii) P-Q alphabet which distinguishes purines (P = A or G) from pyrimidines (Q = C or T); and (iii) a 'control' E-F alphabet (E = A or C; F = G or T). All statistically significant direct repeats within each of the three sequences and all significant block identities (a set of consecutive matching letters) shared by two or more sequences are determined for each alphabet. By contrast to the S-W and E-F alphabets, the P-Q alphabet comparisons reveal an abundance of statistically significant block identities not seen at the nucleotide level. Various interpretations of these P-Q structures with respect to control and functional roles are considered.     

How reliably do amino acid composition comparisons predict sequence similarities between proteins?

A method for comparing amino acid compositions of proteins (Cornish-Bowden, 1977) has been extended to allow proteins of unequal lengths to be compared. The method has been tested by applying it to proteins of known sequence. It tends to exaggerate the amount of difference between unrelated proteins. It is therefore a reliable guide to possible sequence similarities, in that it does not suggest that sequences are similar when they are not, though it sometimes fails to detect genuine similarities. When applied to related proteins the method gives results in good agreement with those predicted. A phylogenetic tree for 37 snake venom toxins has been constructed from their compositions and is similar in most important respects to one constructed from the corresponding sequences.     

The significance of protein sequence similarities

A general method of assessing the significance of scored bestlocal alignments, particularly suited to protein sequence comparisons,is described. The method establishes the parameters describingthe distribution of the best results from any search program,provided that the set is sufficiently large and the majorityof the alignments arise from unrelated sequences. The expectedfrequency of occurrence of any score can then be calculated,together with the number of standard deviations above expectation.These provide sensible measures of significance without additionalsearch operations. However the biological significance of anyalignment or set of alignments does not solely depend on theimprobability of the alignment, but on all relevant factorsknown to the biologist. Received on August 9, 1987; accepted on November 17, 1987     

The diversity ofMalassezia yeasts confirmed by rRNA sequence and nuclear DNA comparisons

One hundred and fourMalassezia strains (52 isolated from humans and 52 from animals) were compared using large subunit (LSU) ribosomal RNA sequence similarity and nuclear DNA complementarity. Eight groups of strains were recognized as genetically distinct species. Each taxon was confirmed by a homogeneous mole % GC and percentages of DNA/DNA reassociations higher than 85%. The non-lipid-dependentMalassezia yeasts were maintained as the unique taxonM. pachydermatis. In contrast, lipid-dependent strains were shown to be distributed among seven species:M. furfur, M. sympodialis andM. species 1–5. These taxa matched remarkably well with morphological and serological differences documented by previous investigators. The LSU rRNA sequences allowed a further intraspecific resolution with most of genomic taxa represented by several closely related sequences:M. pachydermatis counted up to seven sequences,M. furfur four sequences,M. species 1 comprised three sequences andM. species 2 andM. species 5 two sequences. Three species,M. sympodialis, M. species 3 andM. species 4, displayed a unique type of sequence. Thus, the present report demonstrates the usefulness of sequencing for both taxonomic and epidemiological purposes.     

不同产区太子参的rDNA ITS区序列的比较

使用1对引物18SPl和26SP2对采自14个产区的太子参[Pseudostellaria heterophylla(Miq．)Pax ex Pax et Hoffm．]进行ITS基因的PCR扩增和测序。序列分析结果表明,14个产区太子参的ITSl片段长度为219—222bp,ITS2片段长度为235～236bp,5．8S片段长度为155—157bp.除江苏宜兴,江苏句容马梗,江苏南京老鹰山和江苏溧阳等4个产区的ITS序列碱基完全一致外,其他10个产区的ITS序列则有不同的变异,碱基变异数目(包括5．8S编码区)为1—17个。使用UPGMA法重建系统发生树,从分子生物学角度说明了它们的变异程度,为利用ITS区序列的差异鉴别不同产区的太子参提供了依据。     

A test for the statistical significance of DNA sequence similarities for application in databank searches

A method is developed, based on word-searching, which providesa rapid test for the statistical significance of DNA sequencesimilarities for use in databank searching. The method makesallowance for the lengths and dinucleotide compositions of thesequences being compared. A way is also described to calculatethe power of the test, i.e. the probability of detecting a givensimilarity as being statistically significant. The effects onthe power of the test of the scoring method, word length, sequencelength, and sequence composition are examined. A novel scoringmethod is shown to be superior to the method currently usedin most word-searching algorithms. Received on August 3, 1988; accepted on December 12, 1988     

Allozyme and DNA sequence comparisons of nine species of Encephalartos (Zamiaceae)

Phylogenetic relationships between Encephalartos altensteinii Lehmann, E. arenarius R.A. Dyer, E. horridus (Jacquin) Lehmann, E. latifrons Lehmann, E. lehmannii Lehmann, E. longifolius (Jacquin) Lehmann, E. princeps R.A. Dyer and E. trispinosus (Hooker) R.A. Dyer were studied, using E. ferox Bertoloni f. as outgroup. Three continuous and one discontinuous buffer systems were used and gene products of 14 enzyme coding loci were examined by horizontal starch gel-electrophoresis. Genetic variation was studied in a cultivated population of E. lehmannii and the average heterozygosity value for this population is 13.5%, which falls within the range reported for other cycad species. Fixed allele differences between the species studied was not found at any of the loci studied, which suggest that these species are closely related. DNA sequence analysis of rbcL and ITS 1 & 2 genes (1428 and 895 basepairs, respectively) confirmed the close genetic relationships between these taxa. According to ITS and rbcL sequences E. altensteinii and E. princeps are sibling taxa which form a sister group to E. arenarius, E. horridus, E. latifrons, E. lehmannii, E. longifolius, and E. trispinosus. The genetic distances between both groups were 0.12-0.47% for ITS and 0.08-0.16% for rbcL DNA. The results indicate recent (probably pleistocenic) speciation for this group of cycads, and the relationships are discussed with reference to affinities based on morphology and distribution.     

The sequence of human retinal S-antigen reveals similarities with alpha-transducin

The complete amino acid sequence of human retinal S-antigen (48 kDa protein), a retinal protein involved in the visual process has been determined by cDNA sequencing. The largest cDNA was 1590 base pairs (bp) and it contained an entire coding sequence. The similarity of nucleotide sequence between the human and bovine is approximately 80%. The predicted amino acid sequence indicates that human S-antigen has 405 residues and its molecular mass is 45050 Da. The amino acid sequence homology between human and bovine is 81%. There is no overall sequence similarity between S-antigen and other proteins listed in the National Biomedical Research Foundation (NBRF) protein data base. However, local regions of sequence homology with alpha-transducin (T alpha) are apparent including the putative rhodopsin binding and phosphoryl binding sites. In addition, human S-antigen has sequences identical to bovine uveitopathogenic sites, indicating that some types of human uveitis may in part be related to the animal model of experimental autoimmune uveitis (EAU).     

Line geometries for sequence comparisons

Well-known dynamic programming algorithms exist for comparing two finite sequences inO(N ²) time and storage, whereN is the common sequence length. Extensions to the comparison ofM finite sequences requireO((2N) ^M) time and storage, making such algorithms difficult even forM=3. A simple generalization of the sequences makes it possible to obtain some results about the geometry of sequence alignments. These ideas suggest heuristic approaches to problems of comparing several sequences. IfM sequences are known to be related by a binary tree, they can be aligned inO(MN ²) time andO(N ²+NM) storage. This work was supported by a grant from the System Development Foundation.     

DNA sequence comparisons of the human, mouse, and rabbit immunoglobulin kappa gene

A comparative analysis between human, mouse, and rabbit immunoglobulin (Ig) kappa-gene DNA sequences is presented. New formulas for determining the expected length and variance of the longest block identity (a succession of matching nucleotides) between multiple random sequences are given and are used to establish statistical criteria for ascertaining the significance of block identities shared in r out of s sequences. The statistically significant block identities within and between the Ig-kappa-gene sequences are ascertained, and alignment maps based on these similarities are constructed. The human and rabbit sequences (especially in the noncoding regions) and the human and mouse sequences (on the coding regions) show a similarity much stronger than that between the mouse and rabbit sequences. The existence of several highly significant shared oligonucleotides occurring in alignment with each other or with respect to the J- and C-gene segments suggests a configuration of multiple control sites. Discussion and interpretations of the form and distribution of the block identities are given.      

From DNA sequence to improved functionality: using protein sequence comparisons to rapidly design a thermostable consensus phytase

Naturally-occurring phytases having the required level of thermostability for application in animal feeding have not been found in nature thus far. We decided to de novo construct consensus phytases using primary protein sequence comparisons. A consensus enzyme based on 13 fungal phytase sequences had normal catalytic properties, but showed an unexpected 15-22 degrees C increase in unfolding temperature compared with each of its parents. As a first step towards understanding the molecular basis of increased heat resistance, the crystal structure of consensus phytase was determined and compared with that of Aspergillus niger phytase. Aspergillus niger phytase unfolds at much lower temperatures. In most cases, consensus residues were indeed expected, based on comparisons of both three-dimensional structures, to contribute more to phytase stabilization than non-consensus amino acids. For some consensus amino acids, predicted by structural comparisons to destabilize the protein, mutational analysis was performed. Interestingly, these consensus residues in fact increased the unfolding temperature of the consensus phytase. In summary, for fungal phytases apparently an unexpected direct link between protein sequence conservation and protein stability exists.     

Ribosomal DNA and ITS-2 sequence comparisons as a tool for predicting genetic relatedness

The determination of the secondary structure of the internal transcribed spacer (ITS) regions separating nuclear ribosomal RNA genes of Chlorophytes has improved the fidelity of alignment of nuclear ribosomal ITS sequences from related organisms. Application of this information to sequences from green algae and plants suggested that a subset of the ITS-2 positions is relatively conserved. Organisms that can mate are identical at all of these 116 positions, or differ by at most, one nucleotide change. Here we sequenced and compared the ITS-1 and ITS-2 of 40 green flagellates in search of the nearest relative to Chlamydomonas reinhardtii. The analysis clearly revealed one unique candidate, C. incerta. Several ancillary benefits of the analysis included the identification of mislabelled cultures, the resolution of confusion concerning C. smithii, the discovery of misidentified sequences in GenBank derived from a green algal contaminant, and an overview of evolutionary relationships among the Volvocales, which is congruent with that derived from rDNA gene sequence comparisons but improves upon its resolution. The study further delineates the taxonomic level at which ITS sequences, in comparison to ribosomal gene sequences, are most useful in systematic and other studies. Received: 14 February 1997 / Accepted: 28 March 1997     

Primary structure of the catalytic subunit of calf thymus DNA polymerase delta: sequence similarities with other DNA polymerases.

The 125- and 48-kDa subunits of bovine DNA polymerase delta have been isolated by SDS-polyacrylamide gel electrophoresis and demonstrated to be unrelated by partial peptide mapping with N-chlorosuccinimide. A 116-kDa polypeptide, usually present in DNA polymerase delta preparations, was shown to be a degraded form of the 125-kDa catalytic subunit. Amino acid sequence data from Staphylococcus aureus V8 protease, cyanogen bromide, and trypsin digestion of the 125- and 116-kDa polypeptides were used to design primers for the polymerase chain reaction to determine the nucleotide sequence of a full-length cDNA encoding the catalytic subunit of bovine DNA polymerase delta. The predicted polypeptide is 1106 amino acids in length with a calculated molecular weight of 123,707. This is in agreement with the molecular weight of 125,000 estimated from SDS-polyacrylamide gel electrophoresis. Comparison of the deduced amino acid sequence of the catalytic subunit of bovine DNA polymerase delta with that of its counterpart from Saccharomyces cerevisiae showed that the proteins are 44% identical. The catalytic subunit of bovine DNA polymerase delta contains the seven conserved regions found in a number of bacterial, viral, and eukaryotic DNA polymerases. It also contains five additional regions that are highly conserved between bovine and yeast DNA polymerase delta, but these regions share little or no homology with the alpha polymerases. Four of these additional regions are also highly homologous to the herpes virus family of DNA polymerases, whereas one region is not homologous to any other DNA polymerase that has been sequenced thus far.(ABSTRACT TRUNCATED AT 250 WORDS)     

Primate repetitive DNAs: evidence for new satellite DNAs and similarities in non-satellite repetitive DNA sequence properties

Repetitious DNA sequences have been isolated from a number of the primates in both Suborders Anthropoidea and Prosimii by hydroxyapatite chromatography at a C₀t of 10. In addition to finding previously unreported possible AT-rich satellite DNAs in Orangutan, Gibbon, Rhesus and Slow Loris a clear similarity to human DNA was found in the non-satellite repetitious DNA sequence properties of the primates in the Suborder Anthropoidea. This is based on the presence of the hydroxyapatite isolated 1.703 and 1.714 g/cm³ DNA families in CsCl gradients in the analytical ultracentrifuge following renaturation and extensive DNA hyperpolymer network formation. Within the superfamily Hominoidea the amount of the 1.714 g/cm³ DNA family was greater than that of the 1.703 g/cm³ DNA family while the reverse situation was true within the Superfamily Cercopithecoidea. The orangutan 1.703 and 1.714 g/cm³ DNA families were shown to exhibit the same differential reassociation behavior demonstrated previously in human DNA (Marx et al., 1976a). These data are interpreted as preliminary evidence for a similar sequence organization in the Order Primates Suborder Anthropoidea.     

The sequence organization of bovine DNA

The organization of repetitive DNA sequences has been investigated in bovine DNA. Repetitive sequences of all kinds constitute 25% to 30% of the total. Five density satellites constitute about 20% of the genome, and most of the remainder consists of alternating repeating and nonrepeating sequences. The nonrepeating sequences have a very broad size distribution averaging 4,000 nucleotide pairs in length, with the longest exceeding 10,000 nucleotide pairs. The interspersed repetitive sequences are much more nearly homogeneous in size, averaging 350 nucleotide pairs in length, and are divided into 8 to 14 sequence families.     

D-ASSIRC: distributed program for finding sequence similarities in genomes

MOTIVATION: Locating the regions of similarity in a genome requires the availability of appropriate tools such as 'Accelerated Search for SImilar Regions in Chromosomes' (ASSIRC; Vincens et al., Bioinformatics, 14, 715-725, 1998). The aim of this paper is to present different strategies for improving this program by distributing the operations and data to multiple processing units and to assess the efficiency of the different implementations in terms of running time as a function of the number of processing units. RESULTS: The new version D-ASSIRCis based on three alternative strategies of task sharing: (1) a distributed search using the splitting of studied sequences into large overlapping subsequences (strategy ASS); (2) two distributed searches for repeated exact motifs of fixed size either managed by a central processor (strategy AGD) or locally managed by numerous processors (strategy ALD). The result is that the strategy ASSis suitable for a large number of processing units (the time was divided by a factor of 12 when the number of processing units was increased from 1 to 16) wheras the strategy ALDis better for a small set of processors (typically for four or six).The different proposed strategies are efficient for various applications in genomic research, particularly for locating similarities of nucleic sequences in large genomes. AVAILABILITY: D-ASSIRCis freely available by anonymous FTP at ftp://ftp.ens.fr/pub/molbio/dassirc.tar.gz. Sources and binaries for Solaris and Linux are included in the distribution.