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Fast detection of coding regions in short genome sequences: Dragon Promoter Finder Program to recognize vertebrate RNA polymerase II promoters: Vertebrates [7] EasyGene: The gene finder is based on a hidden Markov model (HMM) that is automatically estimated for a new genome. Prokaryotes [8] [9] EuGene: Integrative gene finding: Prokaryotes ...
In 1997, the annotation of the first complete sequence of the E. coli K12 genome used DeCypher Smith-Waterman to determine the function of new translated sequences. [5] [6] [7] In 2002, the rice genome, the first completely sequenced crop, [8] was annotated using DeCypher FrameSearch "to detect and guide the correction of frameshifts caused by ...
The CCDS data set size has continued to increase with both the computational genome annotation updates, which integrate new data sets submitted to the International Nucleotide Sequence Database Collaboration (INSDC), and on ongoing curation activities that supplement or improve upon that annotation.
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances.KEGG is utilized for bioinformatics research and education, including data analysis in genomics, metagenomics, metabolomics and other omics studies, modeling and simulation in systems biology, and translational research in drug development.
The Bioverse framework performs analyses and predictions based on genomic sequence data to annotate and understand the interaction of protein sequence, structure, and function, both at the single molecule as well as at the systems levels. The framework was used to annotate the finished rice genome sequence published in 2005. [21]
BASys (Bacterial Annotation System) is a freely available web server that can be used to perform automated, comprehensive annotation of bacterial genomes. [2] With the advent of next generation DNA sequencing it is now possible to sequence the complete genome of a bacterium (typically ~4 million bases) within a single day.
Expressed sequence tags with their associated sample data. Nucleotide sequence being generated from whole genome sequencing projects at varying stages of assembly, including complete contigs and annotated, fully assembled sequence. Data relating to transcriptomics, such as complementary DNA, with optional annotation.
PacBio and Illumina short‐reads, in combination with 10× Genomics and Bionano data (v1). A total of 949 scaffolds assembled to a final size of 656.77 Mb, with a scaffold N50 of 3.43 Mb (v1), and then further improved to seven pseudo‐chromosomes using Hi‐C sequencing data (v2; scaffold N50: 93.2 Mb, total size in chromosomes: 639.6 Mb).