Search results for "Sequence Alignment"
showing 10 items of 447 documents
Parallel and scalable short-read alignment on multi-core clusters using UPC++
2016
[Abstract]: The growth of next-generation sequencing (NGS) datasets poses a challenge to the alignment of reads to reference genomes in terms of alignment quality and execution speed. Some available aligners have been shown to obtain high quality mappings at the expense of long execution times. Finding fast yet accurate software solutions is of high importance to research, since availability and size of NGS datasets continue to increase. In this work we present an efficient parallelization approach for NGS short-read alignment on multi-core clusters. Our approach takes advantage of a distributed shared memory programming model based on the new UPC++ language. Experimental results using the …
Multiple Protein Sequence Alignment with MSAProbs
2013
Multiple sequence alignment (MSA) generally constitutes the foundation of many bioinformatics studies involving functional, structural, and evolutionary relationship analysis between sequences. As a result of the exponential computational complexity of the exact approach to producing optimal multiple alignments, the majority of state-of-the-art MSA algorithms are designed based on the progressive alignment heuristic. In this chapter, we outline MSAProbs, a parallelized MSA algorithm for protein sequences based on progressive alignment. To achieve high alignment accuracy, this algorithm employs a hybrid combination of a pair hidden Markov model and a partition function to calculate posterior…
Identification and functional expression of HCx31.9, a novel gap junction gene
2002
By combining in silico and bench molecular biology methods we have identified a novel human gap junction gene that encodes a protein designated HCx31.9. We have determined its human chromosomal location and gene structure, and we have identified a putative mouse ortholog, mCx30.2. We have observed the presence of HCx31.9 in human cerebral cortex, liver, heart, spleen, lung, and kidney and the presence of mCx30.2 in mouse cerebral cortex, liver and lung. Moreover, preliminary data on the electrophysiological properties of HCx31.9 have been obtained by functional expression in paired Xenopus oocytes and in transfected N2A cells.
Primary structure and unusual carbohydrate moiety of functional unit 2-c of keyhole limpet hemocyanin (KLH)
1999
Abstract The complete amino acid sequence of the Megathura crenulata hemocyanin functional unit KLH2-c was determined by direct sequencing and matrix-assisted laser desorption ionization mass spectrometry of the protein, and of peptides obtained by cleavage with EndoLysC proteinase, chymotrypsin and cyanogen bromide. This is the first complete primary structure of a functional unit c from a gastropod hemocyanin. KLH2-c consists of 420 amino acid residues. Circular dichroism spectra indicated approx. 31% β-sheet and 29% α-helix contents. A multiple sequence alignment with other molluscan hemocyanin functional units revealed average identities between 41 and 49%, but 55% in case of Octopus he…
Assessing divergence time of Spirulida and Sepiida (Cephalopoda) based on hemocyanin sequences
2011
Abstract The phylogenetic position of the mesopelagic decabrachian cephalopod Spirula is still a matter of debate. Since hemocyanin has successfully been used to calibrate a molecular clock for many molluscan species, a molecular clock was calculated based on this gene with special attention to the cephalopod genera Spirula and Sepia. The obtained partial sequence comprising ca., one third (3567 bp) of the complete gene is similar to that of Sepia officinalis. The molecular clock was calibrated using the splits of Gastropoda–Cephalopoda (ca. 550 ± 50 mya) and Heterobranchia–Vetigastropoda (ca. 380 ± 10 mya). The resulting hemocyanin-based molecular clock is stable, and the estimated diverge…
The Arabidopsis COPT6 Transport Protein Functions in Copper Distribution Under Copper-Deficient Conditions
2013
Copper (Cu), an essential redox active cofactor, participates in fundamental biological processes, but it becomes highly cytotoxic when present in excess. Therefore, living organisms have established suitable mechanisms to balance cellular and systemic Cu levels. An important strategy to maintain Cu homeostasis consists of regulating uptake and mobilization via the conserved family of CTR/COPT Cu transport proteins. In the model plant Arabidopsis thaliana, COPT1 protein mediates root Cu acquisition, whereas COPT5 protein functions in Cu mobilization from intracellular storage organelles. The function of these transporters becomes critical when environmental Cu bioavailability diminishes. Ho…
Similarities and singularities of three DnaK proteins from the cyanobacterium Synechocystis sp. PCC 6803.
2010
In the genome of completely sequenced mesophilic cyanobacterium Synechocystis sp. PCC 6803 three DnaK proteins are encoded, which share a high degree of sequence identity in their N-terminal ATPase region as well as in the adjacent peptide-binding domain. However, as typical for DnaK proteins, the C-termini of the three Synechocystis proteins are highly diverse. To study the functions of the three Synechocystis DnaK proteins in more detail, we have analyzed the abundance of the individual proteins in Synechocystis cells as well as dnaK expression under various stress conditions. The presented results show that all three Synechocystis DnaK proteins interact with the same GrpE nucleotide exch…
Are elicitins cryptograms in plant-oomycete communications?
1999
Stimulation of plant natural defenses is an important challenge in phytoprotection prospects. In that context, elicitins, which are small proteins secreted by Phytophthora and Pythium species, have been shown to induce a hypersensitive-like reaction in tobacco plants. Moreover, these plants become resistant to their pathogens, and thus this interaction constitutes an excellent model to investigate the signaling pathways leading to plant resistance. However, most plants are not reactive to elicitins, although they possess the functional signaling pathways involved in tobacco responses to elicitin. The understanding of factors involved in this reactivity is needed to develop agronomic applica…
Identification of a plasminogen-binding motif in PAM, a bacterial surface protein.
1995
Surface-associated plasmin(ogen) may contribute to the invasive properties of various cells. Analysis of plasmin(ogen)-binding surface proteins is therefore of interest. The N-terminal variable regions of M-like (ML) proteins from five different group A streptococcal serotypes (33, 41, 52, 53 and 56) exhibiting the plasminogen-binding phenotype were cloned and expressed in Escherichia coli. The recombinant proteins all bound plasminogen with high affinity. The binding involved the kringle domains of plasminogen and was blocked by a lysine analogue, 6-aminohexanoic acid, indicating that lysine residues in the M-like proteins participate in the interaction. Sequence analysis revealed that the…
TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics
2016
Nature Methods, 13 (9)