Brief Bioinform. 2013 Jul;14(4):520-6. doi: 10.1093/bib/bbt007. Epub 2013 Feb 22. The Rat Genome Database 2013–data, tools and users.
Laulederkind SJ, Hayman GT, Wang SJ, Smith JR, Lowry TF, Nigam R, Petri V, de Pons J, Dwinell MR, Shimoyama M, Munzenmaier DH, Worthey EA, Jacob HJ.
CoCoNUT is a software tool for performing the following comparative genomics tasks:
Global alignment for two or multiple whole genomes.
Finding regions of high similarity (candidate regions of conserved synteny) among two or multiple genomes.
Comparison of a draft genomes (a draft genome is not a single string but is a set of strings called contigs) to finished or to other draft genome (the current version is limited to at most 2 draft genomes).
cDNA/EST mapping.
Repeat analysis and detection of large segmental duplications.
ARCT (Ageing Research Computational Tools) is a toolkit of Perl modules aimed at bioinformatics, genomics, and gerontology, partly based on the BioPerl package.The aim of ARCT is to allow the comparative genomics of aging. ARCT is a collection of data-mining tools, algorithms, parsers,wrappers, spiders and web applications, etc.
Restauro-G is an open-source rapid genome re-annotation software system , specialized for bacterial genomes. Restauro-G re-annotates a genome by similarity searches utilizing the BLAST-Like Alignment Tool, referring to protein databases such as UniProt KB, NCBI nr, NCBI COGs, Pfam, and PSORTb. Re-annotation by Restauro-G achieved over 98% accuracy for most bacterial chromosomes in comparison with the original manually curated annotation of EMBL releases
Sybil is a web-based software package for comparative genomics, whose primary goal is to facilitate the analysis and visualization of comparative genome data, with a particular emphasis on protein and gene cluster data. Herein, a two-phase protein clustering algorithm, used to generate protein clusters suitable for analysis through Sybil and a method for creating graphical displays of protein or gene clusters that span multiple genomes are described. When combined, these two relatively simple techniques provide the user of the Sybil software (The Institute for Genomic Research [TIGR] Bioinformatics Department) with a browsable graphical display of his or her “input” genomes, showing which genes are conserved based on the parameters supplied to the protein clustering algorithm. For any given protein cluster the graphical display consists of a local alignment of the genomes in which the clustered genes are located. The genomes are arranged in a vertical stack, as in a multiple alignment, and shaded areas are used to connect genes in the same cluster, thus displaying conservation at the protein level in the context of the underlying genomic sequences. The authors have found this display-and slight variants thereof-useful for a variety of annotation and comparison tasks, ranging from identifying “missed” gene models or single-exon discrepancies between orthologous genes, to finding large or small regions of conserved gene synteny, and investigating the properties of the breakpoints between such regions.