BIG Search

BIG Search is a scalable text search engine built based on ElasticSearch (a highly scalable open-source full-text search and analytics engine based on Apache Lucene). It features cross-domain search and facilitates users to gain access to a wide range of biomedical data, not only from BIGD databases but also partner databases throughout the world.

e.g., PRJCA000126;SAMC000385;tp53;EGFR; human; KaKs_Calculator; GenBank

All databases: 7728129

tool: Rapid Identification of Non-human Sequences

  • title: Rapid Identification of Non-human Sequences
  • basicInfo: Rapid identification of non-human sequences (RINS) is an intersection-based pathogen detection... workflow that utilizes a user-provided custom reference genome set for identification of non-human... assembly programs. RINS accurately identifies sequencing reads from intact or mutated non-human genomes... in a dataset and robustly generates contigs with these non-human sequences (Supplementary Material

tool: Prism

  • basicInfo: The rapid growth of sequencing technologies has greatly contributed to our understanding of human... diploid nature of the human genome. Here we describe statistically aided, long-read haplotyping (SLRH... phased information contained in long genomic fragments analyzed by short-read sequencing. For a human... three human genomes into long haplotype blocks 0.2-1 Mbp in length. We apply our method to determine... allele-specific methylation patterns in a human genome and identify hundreds of differentially

tool: microRNA script

  • basicInfo: that human can absorb dietary microRNAs from animal and plant origins while the mechanism remains... unknown. Compelling evidences of microRNAs from rice, milk, and honeysuckle transported to human blood... exogenous microRNAs can be transferred into human circulation and possibly exert functions in... characterize human circulating microRNAs and infer the likelihood that a microRNA will get... transferred into human circulation. For example, 345 dietary microRNAs have been predicted as highly

tool: BLAST Read and Operational Taxonomic Unit Consensus Classifier

  • basicInfo: Eukaryotic microorganisms are important but understudied components of the human microbiome. Here... eight well-characterized human stool samples. A software pipeline pyrosequence data. This study provides a well-characterized tool kit for sequence-based enumeration of eukaryotic organisms in human microbiome samples.

tool: VirusSeq

  • basicInfo: sites in the human genome using next-generation sequencing data. We evaluated VirusSeq on whole...-transcriptome sequencing (RNA-Seq) data of 256 human cancer samples from The Cancer Genome Atlas. Using... sequencing data of human tissue.VirusSeq has been implemented in PERL and is available at http

tool: SUPeR-seq

  • basicInfo: PolyA- RNAs have not been widely analyzed in human pre-implantation embryos due to the scarcity of... characterized during human pre-implantation development.We systematically analyze polyA+ messenger RNAs... (mRNAs) and polyA- RNAs in individual human oocytes and pre-implantation embryos using SUPeR-seq. We de... between human and mouse embryos reveals both high conservation and clear distinction between these... two species. Human pre-implantation embryos generate more types of circRNA compared with mouse

tool: P-clouds

  • basicInfo: consensus element sequences. Using this approach, about half of the human genome has been previously... additional repetitive sequences in the human genome, thus suggesting that 66%-69% of the human genome is...), to detect different sized fragments of the highly abundant human Alu and MIR SINEs. RM can have..., and using it we identified ∼100 Mb of previously unannotated human elements. ESP estimates of new... the human genome consists of substantially more repetitive sequence than previously believed.

tool: SGP2

  • basicInfo: The completion of the sequencing of the mouse genome promises to help predict human genes with... number of false-positive genes in the human genome. Sequence conservation at the protein level with the... genes by comparing the human and mouse genomes is assessed on a number of data sets, including... single-gene data sets, the highly curated human chromosome 22 predictions, and entire genome predictions... human and mouse by comparing the genomes of these two species. Our results suggest that another few

tool: SMIRP

  • basicInfo: attention recently. However, the majority of studies have focused on the human genome. Previous studies... have demonstrated that sensitivity (correctly detecting true miRNA) is sustained when human-trained... specificity (the ability to correctly reject non-miRNA sequences) in non-human genomes. Considering the... prevents the application of most existing tools to non-human genomes, as the number of false.... Substantial improvements in specificity and precision are obtained for four non-human test species

tool: Connectome Visualization Utility

  • basicInfo: In analysis of the human connectome, the connectivity of the human brain is collected from multiple... imaging modalities and analyzed using graph theoretical techniques. The dimensionality of human... the human connectome is limited. The Connectome Visualization Utility (CVU) is a new software package... designed for the visualization and network analysis of human brain networks. CVU complements