Search results for "Sequence alignment"

Short duplication in a cDNA clone of the rbcL gene from Picea abies.

1995

The plastidic rbcL gene encodes the LSU of Rubisco (EC 4.1.1.39), the enzyme that catalyzes CO, fixation during photosynthesis (Hallick and Bottomley, 1983). In higher plants the enzyme structure is commonly given as a hexadecameric structure composed of eight LSUs and eight small subunits. Nucleotide sequence data from the rbcL gene have been used extensively in studies of plant phylogeny and molecular evolution (Morden and Golden, 1991; Pasternak and Glick, 1992). To investigate the expression of the rbcL gene in damaged and undamaged Norway spruce trees (Picea abies), we have isolated a rbcL cDNA clone via reverse transcriptasePCR (Table I). Using the proofreading ability of the DNA poly…

Prion infected rhesus monkeys to study differential transcription of Alu DNA elements and editing of Alu transcripts in neuronal cells and blood cells

2012

Background  Rhesus monkeys were used as a non-human primate model to study small non-coding RNA after infection with human sporadic and variant Creutzfeldt–Jakob prions. Methods  Tissue-specific Alu DNA element transcription and editing of transcripts were assessed in neuronal – and blood cells (Buffy Coat). Results  Tissue/cell-specific transcription and editing patterns were obtained. Active Alu DNA elements belonged to several Alu DNA families, they could be located on several chromosomes, and their genomic sites were identified. Deamination by adenosine deaminase acting on RNA and apolipoprotein B editing complex was found. Conclusions  Different Alu transcription and editing programmes…

rDNA Sequences of <I>Anopheles</I> Species from the Iberian Peninsula and an Evaluation of the 18S rRNA Gene as Phylogenetic Marker in An…

2006

The complete 18S rDNA and internal transcribed spacer (ITS)-2 rDNA sequences were obtained from Anopheles atroparvus Van Thiel and Anopheles plumbeus Stephens from two areas of Spain. The number of nucleotide differences in the 18S rDNA of the two species is high compared with differences in the same gene of other invertebrate vectors. In Anopheles, short 18S rDNA sequences are richer in AT than the longer sequences, which are richer in GC and include extremely GC-biased expanded regions. Four small regions in the variable regions V4 and V7 contain the majority of nucleotide differences. The results did not support the use of partial sequences for relationship analyses. Genetic distances an…

2014

The majority of next-generation sequencing short-reads can be properly aligned by leading aligners at high speed. However, the alignment quality can still be further improved, since usually not all reads can be correctly aligned to large genomes, such as the human genome, even for simulated data. Moreover, even slight improvements in this area are important but challenging, and usually require significantly more computational endeavor. In this paper, we present CUSHAW3, an open-source parallelized, sensitive and accurate short-read aligner for both base-space and color-space sequences. In this aligner, we have investigated a hybrid seeding approach to improve alignment quality, which incorp…

Differential annotation of tRNA genes with anticodon CAT in bacterial genomes.

2006

We have developed three strategies to discriminate among the three types of tRNA genes with anticodon CAT (tRNA(Ile), elongator tRNA(Met) and initiator tRNA(fMet)) in bacterial genomes. With these strategies, we have classified the tRNA genes from 234 bacterial and several organellar genomes. These sequences, in an aligned or unaligned format, may be used for the identification and annotation of tRNA (CAT) genes in other genomes. The first strategy is based on the position of the problem sequences in a phenogram (a tree-like network), the second on the minimum average number of differences against the tRNA sequences of the three types and the third on the search for the highest score value …

Sequences homologous to the hobo transposable element in E strains of Drosophila melanogaster.

2001

Hobo is one of the three Drosophila melanogaster transposable elements, together with the P and I elements, that seem to have recently invaded the genome of this species. Surveys of the presence of hobo in strains from different geographical and temporal origins have shown that recently collected strains contain complete and deleted elements with high sequence similarity (H strains), but old strains lack hobo elements (E strains). Besides the canonical hobo sequences, both H and E strains show other poorly known hobo-related sequences. In the present work, we analyze the presence, cytogenetic location, and structure of some of these sequences in E strains of D. melanogaster. By in situ hybr…

Ubiquitins (polyubiquitin and ubiquitin extension protein) in marine sponges: cDNA sequence and phylogenetic analysis

1999

The complete nucleotide sequences of twoSuberites domunculacDNAs and oneSycon raphanuscDNA, all encoding ubiquitin, have been determined. One cDNA fromS. domunculacodes for polyubiquitin with four tandemly repeated monomeric units and the second cDNA encodes ubiquitin fused to a ribosomal protein of 78 amino acids (aa).S. domunculapossesses at least one additional polyubiquitin gene, from which the last two monomers were also sequenced. All analysed genes fromS. domunculaencode identical ubiquitin proteins, with only one aa difference (Ala19) to the human/higher animals ubiquitin (Pro19). Ubiquitin inS. domunculais identical with the ubiquitin found in another Demospongia,Geodia cydonium. T…

A mammalian gene evolved from the integrase domain of an LTR retrotransposon.

2001

FIG. 1.—Summary of the structure and coding sequence of the human Gin-1 gene. Sequences of human cDNAs with accession numbers XMp003947.2 (a putative full-length cDNA), BE502574, AW173201.1, AW950418.1, AI631948.1, and AA766836.1 were used to deduce and confirm these data. The full-length protein is 522 amino acids long. The Gin-1 coding region spans nucleotides 36153–15345 in the genomic clone NTp002663.4. Arrowheads and the numbers above them, respectively, indicate the positions and lengths of introns. Several Alu repeats were detected within the two largest introns. Bold letters indicate the region homologous to the most conserved part of the IN domain, detailed in figure 2 and used to …

Comparing DNA sequence collections by direct comparison of compressed text indexes

2012

Popular sequence alignment tools such as BWA convert a reference genome to an indexing data structure based on the Burrows-Wheeler Transform (BWT), from which matches to individual query sequences can be rapidly determined. However the utility of also indexing the query sequences themselves remains relatively unexplored. Here we show that an all-against-all comparison of two sequence collections can be computed from the BWT of each collection with the BWTs held entirely in external memory, i.e. on disk and not in RAM. As an application of this technique, we show that BWTs of transcriptomic and genomic reads can be compared to obtain reference-free predictions of splice junctions that have h…

Heterogeneity of HVR-1 quasispecies is predictive of early but not sustained virological response in genotype 1b-infected patients undergoing combine…

2003

ISDR mutation pattern and HVR-1 quasispecies were analyzed in HCV genotype 1b-infected patients treated with either PEG- or STD-IFN plus ribavirin, in order to find virological correlates of therapy outcome. ISDR region analysis, performed at baseline (T0) and at 4 weeks of therapy (T1), indicated that ISDR mutation pattern was not predictive of response to treatment. Moreover, no selection of putative resistant strains in the first month of therapy was observed. Viral load was not correlated with any parameter of HVR-1 heterogeneity. Among the HVR-1 heterogeneity parameters considered, complexity was inversely correlated to viral load decline at T1. In univariate analysis, complexity, prop…