Search results for "DNA sequence"
showing 10 items of 24 documents
AnABlast: Re-searching for Protein-Coding Sequences in Genomic Regions
2019
AnABlast is a computational tool that highlights protein-coding regions within intergenic and intronic DNA sequences which escape detection by standard gene prediction algorithms. DNA sequences with small protein-coding genes or exons, complex intron-containing genes, or degenerated DNA fragments are efficiently targeted by AnABlast. Furthermore, this algorithm is particularly useful in detecting protein-coding sequences with nonsignificant homologs to sequences in databases. AnABlast can be executed online at http://www.bioinfocabd.upo.es/anablast/ .
Comparison of genomic sequences clustering using Normalized Compression Distance and Evolutionary Distance
2008
Genomic sequences are usually compared using evolutionary distance, a procedure that implies the alignment of the sequences. Alignment of long sequences is a long procedure and the obtained dissimilarity results is not a metric. Recently the normalized compression distance was introduced as a method to calculate the distance between two generic digital objects, and it seems a suitable way to compare genomic strings. In this paper the clustering and the mapping, obtained using a SOM, with the traditional evolutionary distance and the compression distance are compared in order to understand if the two distances sets are similar. The first results indicate that the two distances catch differen…
An impaired peroxisomal targeting sequence leading to an unusual bicompartmental distribution of cytosolic epoxide hydrolase
1991
AbstractTo gain an understanding of the mechanism by which the subcellular distribution of cytosolic epoxide hydrolase (cEH) is directed, we have analyzed the carboxy terminal region of rat liver cEH by means of cDNA cloning to define the structure of its possible peroxisomal targeting sequence (PTS). Purified cEH was subjected to peptide analysis following endoproteinase Glu-C digestion and HPLC-separation of the fragments. The obtained sequence information was used to perform PCR experiments resulting in the isolation of a 680 bp cDNA clone encoding the carboxy terminus of cEH. The deduced amino acid sequence displays a terminal tripeptide Ser-Lys-Ile which is highly homologous to the PTS…
First Nationwide Molecular Screening Program in Spain for Patients With Advanced Breast Cancer: Results From the AGATA SOLTI-1301 Study
2021
Anàlisi de seqüències d'ADN; Subtipus PAM50; Genètica molecular Análisis de secuencias de ADN; Subtipo PAM50; Genética molecular DNA sequence analyses; PAM50 subtype; Molecular genetic Background: The SOLTI-1301 AGATA study aimed to assess the feasibility of a multi-institutional molecular screening program to better characterize the genomic landscape of advanced breast cancer (ABC) and to facilitate patient access to matched-targeted therapies in Spain. Methods: DNA sequencing of 74 cancer-related genes was performed using FFPE tumor samples in three different laboratories with three different gene panels. A multidisciplinary advisory board prospectively recommended potential targeted trea…
Aporocotyle mariachristinae n. sp., and A. ymakara VillalbaFernández, 1986 (Digenea: Aporocotylidae) of the pink cusk-eel, Genypterus blacodes (Ophid…
2012
Aporocotyle mariachristinae n. sp. and A. ymakara Villalba & Fernández, 1986 were collected from the bulbus arteriosus and ventral aorta of pink cusk-eels, Genypterus blacodes (Forster, 1801) from Patagonia, Argentina. A. mariachristinae n. sp. can be distinguished from all the species of Aporocotyle by the asymmetrical extension of posterior caeca (right posterior caecum longer, terminating at the area between mid-level of ovary and posterior body end; left posterior caecum shorter, terminating at the area between mid-level of cirrus sac and posterior to reproductive organs), the distribution of spines along the ventro-lateral body margins and the number of testes. The new species clearly …
Molecular markers indicate the phylogenetic identity of southern Brazilian sea asparagus: first record of Salicornia neei in Brazil
2019
Abstract Molecular phylogenetic analyses based on ETS, ITS and atpB - rbcL spacer sequences assessed the phylogenetic status of the southern Brazil sea asparagus species of the genus Salicornia (Salicornioideae, Amaranthaceae). Accessions of Patos Lagoon estuary (32° S) were obtained from wild plants and two pure line lineages, selected from contrasting prostrate (BTH1) and decumbent (BTH2) ecomorphotypes found locally. Patos Lagoon wild plants, BTH1 and BTH2 f4 progenies showed 100% identical sequences for the atpB - rbcL and ITS spacers, only two mutations for ETS. Comparison of the sequences of these three markers with GenBank records confirmed the identity of Brazilian accessions as Sal…
Salinity and Bacterial Diversity: To What Extent Does the Concentration of Salt Affect the Bacterial Community in a Saline Soil?
2014
In this study, the evaluation of soil characteristics was coupled with a pyrosequencing analysis of the V2-V3 16S rRNA gene region in order to investigate the bacterial community structure and diversity in the A horizon of a natural saline soil located in Sicily (Italy). The main aim of the research was to assess the organisation and diversity of microbial taxa using a spatial scale that revealed physical and chemical heterogeneity of the habitat under investigation. The results provided information on the type of distribution of different bacterial groups as a function of spatial gradients of soil salinity and pH. The analysis of bacterial 16S rRNA showed differences in bacterial compositi…
Two changes of the same nucleotide confer resistance to diuron and antimycin in the mitochondrial cytochrome b gene of Schizosaccharomyces pombe
1988
AbstractDiuron (3-(3,4-dichlorophenyl)-1,1-dimethylurea) and antimycin, both inhibitors of mitochondrial respiration, block electron flow between cytochromes b and c1. Mutants resistant to either drug have been selected using Schizosaccharomyces pombe strains with an extrachromosomally inherited mutator. In analogy to Saccharomyces cerevisiae these mutational sites were assumed to map in the cytochrome b gene. DNA sequence analysis showed that two changes in the same nucleotide are responsible for resistance to antimycin and diuron. Analysis of resistant and sensitive progeny of crosses between the mutants and the wild type confirmed the correlation between mutational alteration and resista…
A new feature selection strategy for K-mers sequence representation
2014
DNA sequence decomposition into k-mers (substrings of length k) and their frequency counting, defines a mapping of a sequence into a numerical space by a numerical feature vector of fixed length. This simple process allows to compute sequence comparison in an alignment free way, using common similarities and distance functions on the numerical codomain of the mapping. The most common used decomposition uses all the substrings of length k making the codomain of exponential dimension. This obviously can affect the time complexity of the similarity computation, and in general of the machine learning algorithm used for the purpose of sequence classification. Moreover, the presence of possible n…
Alignment free Dissimilarities for sequence classification
2015
One way to represent a DNA sequence is to break it down into substrings of length L, called L-tuples, and count the occurence of each L-tuple in the sequence. This representation defines a mapping of a sequence into a numerical space by a numerical feature vector of fixed length, that allows to measure sequence similarity in an alignment free way simply using disssimilarity functions between vectors. This work presents a benchmark study of 4 alignment free disssimilarity functions between sequences, computed on their L-tuples representation, for the purpose of sequence classification. In our experiments, we have tested the classes of geometric-based, correlation-based and information-based …