Biomedical subjects

M Attimonelli

Publications and source records attributed to M Attimonelli.

6 recordsLinked to original sources

PubMed1992

WORDUP: an efficient algorithm for discovering statistically significant patterns in DNA sequences.

We present here a fast and sensitive method designed to isolate short nucleotide sequences which have non-random statistical properties and may thus be biologically active. It is based on a first order Markov analysis and allows us to detect statistically significant sequence motifs from six to ten nucleotides long which are significantly shared (or avoided) in the sequences under investigation. This method has been tested on a set of 521 sequences extracted from the Eukaryotic Promoter Database (2). Our results demonstrate the accuracy and the efficiency of the method in that the sequence motifs which are known to act as eukaryotic promoters, such as the TATA-box and the CAAT-box, were clearly identified. In addition we have found other statistically significant motifs, the biological roles of which are yet to be clarified.

Algorithms↗

PubMed1992

A simple method for global sequence comparison.

A simple method of sequence comparison, based on a correlation analysis of oligonucleotide frequency distributions, is here shown to be a reliable test of overall sequence similarity. The method does not involve sequence alignment procedures and permits the rapid screening of large amounts of sequence data. It identifies those sequences which deserve more careful analysis of sequence similarity at the level of resolution of the single nucleotide. It uses observed quantities only and does not involve the adoption of any theoretical model.

Algorithms↗

PubMed1992

A statistical method for detecting regions with different evolutionary dynamics in multialigned sequences.

We describe a stochastic method for tracing the evolutionary pattern of multialigned sequences. This method allows us to detect gene regions with distinct evolutionary dynamics, e.g., regions that significantly deviate from the expected behavior. Accurate detection of hypervariable or hyperconstrained regions may provide useful information on the structure/function relationship of biosequences. This information can help localize functional constraints. In addition, the selection of distinct evolutionary dynamics may assist in the correct use of biosequences as reliable molecular clocks.

Animals↗

PubMed1990

Reorganization and merging of the EMBL and GenBank keyword indexes in a tree structure for more efficient retrieval of nucleic acid sequences.

EMBL and GenBank keyword indexes have no hierarchical structure. In this paper we present a method for merging and reorganizing them in a tree structure whose primary roots are the keywords 'protein', 'DNA', 'RNA', and 'unclassified'. Synonymous keywords have been grouped together and erroneous keywords have been corrected. This taxonomic organization of keywords results in a more extensive and efficient retrieval which is further aided by "synonyms declaration". The tree has been produced using the computer programs GENPOINT and CREANET.

Abstracting and Indexing↗

PubMed1990

Estimation of protein secondary structure from circular dichroism spectra: a critical examination of the CONTIN program.

The computer program CONTIN uses the Provencher and Glöckner procedure to calculate protein secondary structure from circular dichroism spectra. We have tested this program with peptides and proteins in which unfolding was either induced by denaturing treatment or was already present. Results indicate that the program does not clearly discriminate between the ordered and the unordered states of a protein.

Circular Dichroism↗

PubMed1985

Multisequence comparisons in protein coding genes. Search for functional constraints.

A very powerful method for detecting functional constraints operative in biological macromolecules is presented. This method entails performing a base permanence analysis of protein coding genes at each codon position simultaneously in different species. It calculates the degree of permanence of subregions of the gene by dividing it into segments, c codons long, counting how many sites remain unchanged in each segment among all species compared. By comparing the base permanence among several sequences with the expectations based on a stochastic evolutionary process, gene regions showing different degrees of conservation can be selected. This means that wherever the permanence deviates significantly from the expected value generated by the simulation, the corresponding regions are considered "constrained" or "hypervariable". The constrained regions are of two types: alpha and beta. The alpha regions result from constraints at the amino acid level, whereas the beta regions are those probably involved in "control" processing. The method has been applied to mitochondrial genes coding for subunit 6 of the ATPase and subunit 1 of the cytochrome oxidase in four mammalian species: human, rat, mouse, and cow. In the two mitochondrial genes a few regions that are highly conserved in all codon positions have been identified. Among these regions a sequence, common to both genes, that is complementary to a strongly conserved region of 12S rRNA has been found. This method can also be of great help in studying molecular evolution mechanisms.

Amino Acid Sequence↗