GSD :: Genomic Signature Database

Welcome to GSD!

Genomic Signature Database (GSD) contains a series of databases that analyze and compare genomic sequences based on the "signature" of the sequences, instead of the sequence homology-based methods. Codon usages and oligonucleotide frequences can both be considered variants of sequence signatures. Analysis and comparison of sequences based on the signatures are thus not limited to their sizes and origins (homologous sources).

Below is a list of the signature-based sequence databases that are available at GSD:

Microbial Genome Codon Usage Database (MGCUD)
MGCUD provides interactive tools for comparing the "genome-wide" codon usage patterns of all the microbial genomes available at NCBI. It also allows comparing the codon usage patterns of user-uploaded sequecnes with those of selected genomes.
Non-redundant Codong Usage Database (NRCUD)
NRCUD provides interactive tools for studying the "organism-wide" and "non-redundant"codon usage patterns calculated based on all the protein coding sequences of an organism (taxon) that are available in the NCBI RefSeq database. It also allows comparing the codon usage patterns of user-uploaded sequecnes with those of selected organisms.
Non-redundant Nucleotide Usage Database (NUGET)
NUGET is a comparative genomics tool that provides clustering software for comparing the usage frequencies of oligo-nucleotide seqeunces among selected genomes. Frequency data of up to 4-letter words (tetra-nucleotide) are calculated from the non-redundant genomic DNA sequences that are available in the NCBI RefSeq database.
Genomic Tetranucleotide Composition Analysis (GTCA)
GTCA studies the variation of tetranucleotide compositions in microbial genomes .
A Sequence Signature Search Tool (ASSIST)
ASSIST is a sequence signature search tool that finds the closest matches of the query DNA sequence among the database sequences by calculating their tetranucleotide profile similarities on the fly. ASSIST can analyze an unknown sequence provided by users and predict the most-likely taxonomic origins. ASSIST is a sequence data-mining tool that complements the homologous search methods such as BLAST, especially when no matches can be found by sequence homology.