DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication
We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation s...2365 days ago
phyloXML: XML for evolutionary biology and comparative genomics
...t values, and gene duplication and speciation events. Using these standardized elements allows interoperability between various applications and databases. Furthermore, both due to ext...2350 days ago
BEAP: Blast Extension and Assembly Program
...is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide databases in an attempt to obtain all s...2156 days ago
CGView - Circular Genome Viewer
...ng. The feature labels in maps can be hyperlinked to external resources, allowing CGView maps to be integrated with existing web site content or databases. For examples of the various...2147 days ago
miREM: an expectation-maximization approach for prioritizing miRNAs associated with gene-set
From list of genes... ... to microRNAs Using established miRNA-interaction databases, miREM combines hypergeometric and expectation-maximization algorithms to sieve through your genetic data for microRNA signatures https://bioinfo-csi.nus.edu.sg/mirem2/2090 days ago
KOBAS: a web server for gene/protein functional annotation and functional gene set enrichment
...dule). For Annotate module, it accepts gene list as input, including IDs or sequences, and generates annotations for each gene based on multiple databases about pathways, diseases, and...2026 days ago
2021 days ago
BLAST options, setting and defaults
...significantly improved by Altschul et al. (1997). It is a very fast search algorithm that is used to separately search protein or DNA databases. BLAST is best used for seque...1974 days ago
SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences
The software package SiLiX implements an ultra-efficient algorithm for the clustering of homologous sequences, based on single transitive links (single linkage) wit...1972 days ago
Biotite: A general framework for computational biology
...hon. Biotite consists of four sub packages: sequence, structure, databases, and application. The se...lysis respectively, database downloads files from the other databases such as RCSB PDB, and ap...1967 days ago