RESUMO
MOTIVATION: The genomic era in molecular biology has brought on a rapidly widening gap between the amount of sequence data and first-hand experimental characterization of proteins. Fortunately, the theory of evolution provides a simple solution: functional and structural information can be transferred between homologous proteins. Sequence similarity searching followed by k-nearest neighbor classification is the most widely used tool to predict the function or structure of anonymous gene products that come out of genome sequencing projects. RESULTS: We present a novel word filter, suffix array neighborhood search (SANS), to identify protein sequence similarities in the range of 50-100% identity with sensitivity comparable to BLAST and 10 times the speed of USEARCH. In contrast to these previous approaches, the complexity of the search is proportional only to the length of the query sequence and independent of database size, enabling fast searching and functional annotation into the future despite rapidly expanding databases. AVAILABILITY AND IMPLEMENTATION: The software is freely available to non-commercial users from our website http://ekhidna.biocenter.helsinki.fi/downloads/sans. CONTACT: liisa.holm@helsinki.fi.
Assuntos
Análise de Sequência de Proteína/métodos , Homologia de Sequência de Aminoácidos , Algoritmos , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Bases de Dados de Proteínas , Genoma , Metagenoma , Alinhamento de Sequência , SoftwareRESUMO
We report the complete and annotated genome sequence of the plant-pathogenic enterobacterium Pectobacterium sp. strain SCC3193, a model strain isolated from potato in Finland. The Pectobacterium sp. SCC3193 genome consists of a 5,164,411-bp [corrected] chromosome, with no plasmids.
Assuntos
DNA Bacteriano/química , DNA Bacteriano/genética , Genoma Bacteriano , Pectobacterium/genética , Análise de Sequência de DNA , Finlândia , Dados de Sequência Molecular , Pectobacterium/isolamento & purificação , Doenças das Plantas/microbiologia , Solanum tuberosum/microbiologiaRESUMO
Lactobacillus crispatus is a common member of the beneficial microbiota present in the vertebrate gastrointestinal and human genitourinary tracts. Here, we report the genome sequence of L. crispatus ST1, a chicken isolate displaying strong adherence to vaginal epithelial cells.
Assuntos
Genoma Bacteriano/genética , Lactobacillus/genéticaRESUMO
Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.