32 research outputs found
Parallel approach to sliding window sums
Sliding window sums are widely used in bioinformatics applications, including
sequence assembly, k-mer generation, hashing and compression. New vector
algorithms which utilize the advanced vector extension (AVX) instructions
available on modern processors, or the parallel compute units on GPUs and
FPGAs, would provide a significant performance boost for the bioinformatics
applications. We develop a generic vectorized sliding sum algorithm with
speedup for window size w and number of processors P is O(P/w) for a generic
sliding sum. For a sum with commutative operator the speedup is improved to
O(P/log(w)). When applied to the genomic application of minimizer based k-mer
table generation using AVX instructions, we obtain a speedup of over 5X.Comment: 10 pages, 5 figure
Derivatives of Isoindoline, Synthesis and Biological Activity. II. Biological Activity of Derivatives of Isoindoline
Derivati izoindolina pokazuju vrlo razliÄita bioloÅ”ka djelovanja in vitro, a neki djeluju i u uvjetima in vivo. Stoga se može oÄekivati da Äe istraživanja u buduÄnosti dovesti i do uÄinkovitih lijekova za razliÄite vrste bolesti. Pokazuju nesteroidnu protuupalnu aktivnost, antihipertenzivno djelovanje, anksiolitiÄko, antipsihotiÄko i antikonvulzivno djelovanje. Djeluju kao lokalni anestetici, vazodilatatori te se vežu na dopaminske i serotononske receptore. Ubrajaju se takoÄer u skupinu antidijabetika inhibirajuÄi dipeptidil-peptidaze. Metalni kompleksi izoindolina i njegovih derivata djeluju poput enzima katalaze koji Å”titi stanice od Å”tetnog djelovanja vodikova peroksida te djeluju i kao inhibitori protein-kinaza. Osim ostalih znaÄajno je njihovo antitumorsko djelovanje na stanice leukemije, karcinoma debelog crijeva, epidermalnog karcinoma te karcinoma jajnika. Oni takoÄer inhibiraju enzime koji potiÄu rast tumorskih stanica kao Å”to su histon deacetilaza te receptori tirozin-kinaze i krvožilnog endotelnog Äimbenika rasta (VEGF-R2).Derivatives of isoindolines are a group of nitrogen heterocyclic compounds that are less represented in scientific literature than other heterocyclic compounds containing the nitrogen atom. Natural derivatives of isoindolines were first isolated in the early 1960\u27s and showed various interesting biological activity, e.g. staurosporine indicating antimicrobial, hypotensive, and cytotoxic activity, and acts as thrombocytes aggregation inhibitor and protein kinase inhibitor. Also, there are reports of their application in herbicide and dye industries. Due to these findings, isoindolines received much attention from synthetic organic chemists, and thus new synthetic methods were developed. Most of the methods include phthalaldehyde and corresponding aliphatic and aromatic amines as starting material. Products of these reactions are highly dependent on the reaction conditions, and differently substituted isoindolines are isolated. Synthetic methods starting from other compounds include phthalonitrile, phthalanhydride and phthalaldehyde acid as well as multicomponent reactions. They are also applied as ligands in coordination chemistry, which enables the modelling of
three-dimensional structures with desirable areal properties
Annotated mitochondrial genome with Nanopore R9 signal for <i>Nippostrongylus brasiliensis</i>
Nippostrongylus brasiliensis, a nematode parasite of rodents, has a parasitic life cycle that is an extremely useful model for the study of human hookworm infection, particularly in regards to the induced immune response. The current reference genome for this parasite is highly fragmented with minimal annotation, but new advances in long-read sequencing suggest that a more complete and annotated assembly should be an achievable goal. We de-novoĀ assembled a single contig mitochondrial genome from N. brasiliensisĀ using MinION R9 nanopore data. The assembly was error-corrected using existing Illumina HiSeq reads, and annotated in full (i.e. gene boundary definitions without substantial gaps) by comparing with annotated genomes from similar parasite relatives. The mitochondrial genome has also been annotated with a preliminary electrical consensus sequence, using raw signal data generated from a Nanopore R9 flow cell
Accurate detection of complex structural variations using single-molecule sequencing
Structural variations are the greatest source of genetic variation, but they remain poorly understood because of technological limitations. Single-molecule long-read sequencing has the potential to dramatically advance the field, although high error rates are a challenge with existing methods. Addressing this need, we introduce open-source methods for long-read alignment (NGMLR; https://github.com/philres/ngmlr ) and structural variant identification (Sniffles; https://github.com/fritzsedlazeck/Sniffles ) that provide unprecedented sensitivity and precision for variant detection, even in repeat-rich regions and for complex nested events that can have substantial effects on human health. In several long-read datasets, including healthy and cancerous human genomes, we discovered thousands of novel variants and categorized systematic errors in short-read approaches. NGMLR and Sniffles can automatically filter false events and operate on low-coverage data, thereby reducing the high costs that have hindered the application of long reads in clinical and research settings
Derivatives of Isoindoline, Synthesis and Biological Activity. I. Natural and Synthetic Derivatives of Isoindoline
Derivati izoindolina pripadaju skupini duÅ”ikovih heterocikliÄkih spojeva koji su manje zastupljeni u literaturi od ostalih duÅ”ikovih heterocikliÄkih spojeva. Prvi prirodni derivati izoindolina izolirani su u drugoj polovici proÅ”log stoljeÄa te su pokazali razliÄita interesantna bioloÅ”ka djelovanja, npr. staurosporin koji pokazuje antimikrobno, hipotenzivno i citotoksiÄno djelovanje te djeluje kao inhibitor agregacije trombocita i inhibitor protein-kinaze. Zbog tih saznanja porastao je interes za kemiju izoindolina i pronaÄene su razliÄite sintetske metode njihova dobivanja. NajviÅ”e su zastupljene sinteze iz ftalaldehida i odgovarajuÄih alifatskih i aromatskih amina kao polaznih spojeva. Sinteze iz ostalih polaznih spojeva ukljuÄuju ftalonitril, ftalanhidrid i ftalaldehidnu kiselinu te viÅ”ekomponentne reakcije. Izoindolin i njegovi derivati zastupljeni su kao ligandi u kemiji metalnih kompleksa. Tako su prireÄeni metalni kompleksi koji omoguÄuju dizajniranje ciljanih trodimenzijskih struktura Å”to se može primijeniti u raznim podruÄjima koordinativne kemije, ali i u dizajniranju bioloÅ”ki aktivnih spojeva s toÄno odreÄenim prostornim svojstvima.Derivatives of isoindolines are a group of nitrogen heterocyclic compounds that are less represented in scientific literature than other heterocyclic compounds containing the nitrogen atom. Natural derivatives of isoindolines were first isolated in the early 1960\u27s and showed various interesting biological activity, e.g. staurosporine indicating antimicrobial, hypotensive, and cytotoxic activity, and acts as thrombocytes aggregation inhibitor and protein kinase inhibitor. Also, there are reports of their application in herbicide and dye industries. Due to these findings, isoindolines received much attention from synthetic organic chemists, and thus new synthetic methods were developed. Most of the methods include phthalaldehyde and corresponding aliphatic and aromatic amines as starting material. Products of these reactions are highly dependent on the reaction conditions, and differently substituted isoindolines are isolated. Synthetic methods starting from other compounds include phthalonitrile, phthalanhydride and phthalaldehyde acid as well as multicomponent reactions. They are also applied as ligands in coordination chemistry, which enables the modelling of
three-dimensional structures with desirable areal properties