Homology induction: the use of machine learning to improve sequence similarity searches.

abstract：BACKGROUND:Microsatellite (simple sequence repeat - SSR) and single nucleotide polymorphism (SNP) markers are two types of important genetic markers useful in genetic mapping and genotyping. Often, large-scale genomic research projects require high-throughput computer-assisted primer design. Numerous such web-based or ...

journal_title：BMC bioinformatics

authors： You FM,Huo N,Gu YQ,Luo MC,Ma Y,Hane D,Lazo GR,Dvorak J,Anderson OD

更新日期：2008-05-29 00:00:00

abstract：BACKGROUND:Finishing is the process of improving the quality and utility of draft genome sequences generated by shotgun sequencing and computational assembly. Finishing can involve targeted sequencing. Finishing reads may be incorporated by manual or automated means. One automated method uses targeted addition by local...

journal_title：BMC bioinformatics

authors： Koren S,Miller JR,Walenz BP,Sutton G

更新日期：2010-09-10 00:00:00

abstract：BACKGROUND:Decreasing costs of DNA sequencing have made prokaryotic draft genome sequences increasingly common. A contig scaffold is an ordering of contigs in the correct orientation. A scaffold can help genome comparisons and guide gap closure efforts. One popular technique for obtaining contig scaffolds is to map con...

journal_title：BMC bioinformatics

authors： Dias Z,Dias U,Setubal JC

更新日期：2012-05-14 00:00:00

abstract：BACKGROUND:DNA methylation patterns store epigenetic information in the vast majority of eukaryotic species. The relatively high costs and technical challenges associated with the detection of DNA methylation however have created a bias in the number of methylation studies towards model organisms. Consequently, it rema...

journal_title：BMC bioinformatics

authors： Bulla I,Aliaga B,Lacal V,Bulla J,Grunau C,Chaparro C

更新日期：2018-03-27 00:00:00

abstract：BACKGROUND:Reproducibility of results can have a significant impact on the acceptance of new technologies in gene expression analysis. With the recent introduction of the so-called next-generation sequencing (NGS) technology and established microarrays, one is able to choose between two completely different platforms f...

journal_title：BMC bioinformatics

authors： Stiglic G,Bajgot M,Kokol P

更新日期：2010-04-08 00:00:00

abstract：BACKGROUND:Cryo-electron tomography (cryo-ET) enables the 3D visualization of cellular organization in near-native state which plays important roles in the field of structural cell biology. However, due to the low signal-to-noise ratio (SNR), large volume and high content complexity within cells, it remains difficult a...

journal_title：BMC bioinformatics

authors： Li R,Zeng X,Sigmund SE,Lin R,Zhou B,Liu C,Wang K,Jiang R,Freyberg Z,Lv H,Xu M

更新日期：2019-03-29 00:00:00

abstract：BACKGROUND:De Bruijn graphs are key data structures for the analysis of next-generation sequencing data. They efficiently represent the overlap between reads and hence, also the underlying genome sequence. However, sequencing errors and repeated subsequences render the identification of the true underlying sequence dif...

journal_title：BMC bioinformatics

authors： Steyaert A,Audenaert P,Fostier J

更新日期：2020-09-14 00:00:00

abstract：BACKGROUND:High-resolution tandem mass spectra can now be readily acquired with hybrid instruments, such as LTQ-Orbitrap and LTQ-FT, in high-throughput shotgun proteomics workflows. The improved spectral quality enables more accurate de novo sequencing for identification of post-translational modifications and amino ac...

journal_title：BMC bioinformatics

authors： Pan C,Park BH,McDonald WH,Carey PA,Banfield JF,VerBerkmoes NC,Hettich RL,Samatova NF

更新日期：2010-03-05 00:00:00

abstract：BACKGROUND:Long-range interactions between regulatory DNA elements such as enhancers, insulators and promoters play an important role in regulating transcription. As chromatin contacts have been found throughout the human genome and in different cell types, spatial transcriptional control is now viewed as a general mec...

journal_title：BMC bioinformatics

authors： Rousseau M,Fraser J,Ferraiuolo MA,Dostie J,Blanchette M

更新日期：2011-10-25 00:00:00

abstract：BACKGROUND:Infections are often associated to comorbidity that increases the risk of medical conditions which can lead to further morbidity and mortality. SARS is a threat which is similar to MERS virus, but the comorbidity is the key aspect to underline their different impacts. One UK doctor says "I'd rather have HIV ...

journal_title：BMC bioinformatics

authors： Moni MA,Liò P

更新日期：2014-10-24 00:00:00

abstract：BACKGROUND:Analyzing the amino acid sequence of an intrinsically disordered protein (IDP) in an evolutionary context can yield novel insights on the functional role of disordered regions and sequence element(s). However, in the case of many IDPs, the lack of evolutionary conservation of the primary sequence can hamper ...

journal_title：BMC bioinformatics

authors： Varadi M,Guharoy M,Zsolyomi F,Tompa P

更新日期：2015-05-13 00:00:00

abstract：BACKGROUND:Comparative genomics has become an essential approach for identifying homologous gene candidates and their functions, and for studying genome evolution. There are many tools available for genome comparisons. Unfortunately, most of them are not applicable for the identification of unique genes and the inferen...

journal_title：BMC bioinformatics

authors： Lu G,Jiang L,Helikar RM,Rowley TW,Zhang L,Chen X,Moriyama EN

更新日期：2006-12-12 00:00:00

abstract：BACKGROUND:SNP genotyping microarrays have revolutionized the study of complex disease. The current range of commercially available genotyping products contain extensive catalogues of low frequency and rare variants. Existing SNP calling algorithms have difficulty dealing with these low frequency variants, as the under...

journal_title：BMC bioinformatics

authors： Liu R,Dai Z,Yeager M,Irizarry RA,Ritchie ME

更新日期：2014-05-23 00:00:00

abstract：BACKGROUND:Protein remote homology detection and fold recognition are central problems in bioinformatics. Currently, discriminative methods based on support vector machine (SVM) are the most effective and accurate methods for solving these problems. A key step to improve the performance of the SVM-based methods is to f...

journal_title：BMC bioinformatics

authors： Liu B,Wang X,Lin L,Dong Q,Wang X

更新日期：2008-12-01 00:00:00

abstract：BACKGROUND:Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain datab...

journal_title：BMC bioinformatics

authors： Truong K,Ikura M

更新日期：2003-05-06 00:00:00

abstract：BACKGROUND:The identification of differentially expressed genes (DEGs) from Affymetrix GeneChips arrays is currently done by first computing expression levels from the low-level probe intensities, then deriving significance by comparing these expression levels between conditions. The proposed PL-LM (Probe-Level Linear ...

journal_title：BMC bioinformatics

authors： Lemieux S

更新日期：2006-08-25 00:00:00

abstract：:Environmental shotgun sequencing (ESS) has potential to give greater insight into microbial communities than targeted sequencing of 16S regions, but requires much higher sequence coverage. The advent of next-generation sequencing has made it feasible for the Human Microbiome Project and other initiatives to generate E...

journal_title：BMC bioinformatics

authors： Ander C,Schulz-Trieglaff OB,Stoye J,Cox AJ

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:High throughput DNA/RNA sequencing has revolutionized biological and clinical research. Sequencing is widely used, and generates very large amounts of data, mainly due to reduced cost and advanced technologies. Quickly assessing the quality of giga-to-tera base levels of sequencing data has become a routine ...

journal_title：BMC bioinformatics

authors： Chanumolu SK,Albahrani M,Otu HH

更新日期：2019-08-15 00:00:00

abstract：BACKGROUND:The exponential growth of gigantic biological data from various sources, such as protein-protein interaction (PPI), genome sequences scaffolding, Mass spectrometry (MS) molecular networking and metabolic flux, demands an efficient way for better visualization and interpretation beyond the conventional, two-d...

journal_title：BMC bioinformatics

authors： Wang Q,Tang B,Song L,Ren B,Liang Q,Xie F,Zhuo Y,Liu X,Zhang L

更新日期：2013-11-14 00:00:00

abstract：BACKGROUND:The Immunoglobulins (IG) and the T cell receptors (TR) play the key role in antigen recognition during the adaptive immune response. Recent progress in next-generation sequencing technologies has provided an opportunity for the deep T cell receptor repertoire profiling. However, a specialised software is req...

journal_title：BMC bioinformatics

authors： Nazarov VI,Pogorelyy MV,Komech EA,Zvyagin IV,Bolotin DA,Shugay M,Chudakov DM,Lebedev YB,Mamedov IZ

更新日期：2015-05-28 00:00:00

abstract：:We developed a new computational technique called Step-Level Differential Response (SLDR) to identify genetic regulatory relationships. Our technique takes advantages of functional genomics data for the same species under different perturbation conditions, therefore complementary to current popular computational techn...

journal_title：BMC bioinformatics

authors： Yue Z,Wan P,Huang H,Xie Z,Chen JY

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:The development of high-throughput sequencing and analysis has accelerated multi-omics studies of thousands of microbial species, metagenomes, and infectious disease pathogens. Omics studies are enabling genotype-phenotype association studies which identify genetic determinants of pathogen virulence and drug...

journal_title：BMC bioinformatics

authors： Singh I,Kuscuoglu M,Harkins DM,Sutton G,Fouts DE,Nelson KE

更新日期：2019-01-07 00:00:00

abstract：BACKGROUND:Due to recent technology advancements, disease related knowledge is growing rapidly. It becomes nontrivial to go through all published literature to identify associations between human diseases and genetic, environmental, and life style factors, disease symptoms, and treatment strategies. Here we report DLAD...

journal_title：BMC bioinformatics

authors： Shen J,Vasaikar S,Zhang B

更新日期：2018-12-28 00:00:00

abstract：BACKGROUND:Polymorphic variants and mutations disrupting canonical splicing isoforms are among the leading causes of human hereditary disorders. While there is a substantial evidence of aberrant splicing causing Mendelian diseases, the implication of such events in multi-genic disorders is yet to be well understood. We...

journal_title：BMC bioinformatics

authors： Churbanov A,Vorechovský I,Hicks C

更新日期：2010-01-12 00:00:00

abstract：BACKGROUND:In recent years, a considerable amount of research effort has been directed to the analysis of biological networks with the availability of genome-scale networks of genes and/or proteins of an increasing number of organisms. A protein-protein interaction (PPI) network is a particular biological network which...

journal_title：BMC bioinformatics

authors： Turanalp ME,Can T

更新日期：2008-06-11 00:00:00

abstract：BACKGROUND:Here we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. Our goals in building PSAT were to (1) create an extensible platform for integration of multiple sequence-based bioinformatics...

journal_title：BMC bioinformatics

authors： Leung E,Huang A,Cadag E,Montana A,Soliman JL,Zhou CL

更新日期：2016-01-20 00:00:00

abstract：BACKGROUND:Infectious disease modeling and computational power have evolved such that large-scale agent-based models (ABMs) have become feasible. However, the increasing hardware complexity requires adapted software designs to achieve the full potential of current high-performance workstations. RESULTS:We have found l...

journal_title：BMC bioinformatics

authors： Willem L,Stijven S,Tijskens E,Beutels P,Hens N,Broeckhove J

更新日期：2015-06-02 00:00:00

abstract：BACKGROUND:Cyclic nucleotides are ubiquitous intracellular messengers. Until recently, the roles of cyclic nucleotides in plant cells have proven difficult to uncover. With an understanding of the protein domains which can bind cyclic nucleotides (CNB and GAF domains) we scanned the completed genomes of the higher plan...

journal_title：BMC bioinformatics

authors： Bridges D,Fraser ME,Moorhead GB

更新日期：2005-01-11 00:00:00

abstract：BACKGROUND:Interaction of a drug or chemical with a biological system can result in a gene-expression profile or signature characteristic of the event. Using a suitably robust algorithm these signatures can potentially be used to connect molecules with similar pharmacological or toxicological properties by gene express...

journal_title：BMC bioinformatics

authors： Zhang SD,Gant TW

更新日期：2008-06-02 00:00:00

abstract：BACKGROUND:Most human genes produce several transcripts with different exon contents by using alternative promoters, alternative polyadenylation sites and alternative splice sites. Much effort has been devoted to describing known gene transcripts through the development of numerous databases. Nevertheless, owing to the...

journal_title：BMC bioinformatics

authors： de la Grange P,Dutertre M,Correa M,Auboeuf D

更新日期：2007-06-04 00:00:00