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The Appendices also provide a number of tools and resources that provide greaterhints for the retroviral genome structure. Appendix 2 contains a brief survey ofthe use of the different nucleic acid and protein alignment programs that havebeen developed for the alignment and identification of retroviral genomes. Theappendix includes a listing of the different programs and the advantages anddisadvantages of each. The listing also includes links to a number of excellentresources with their current release version, including the NCBIGenBank database. The retroviral nucleotide database at NCBI,, is composed ofall known retroviral and retrotransposon sequences, and provides a means ofseeding the database with new sequences. See http://www.ncbi.nlm.nih.gov/genomes/FLY/ for detailedinformation about the database and its release version. The retroviral genome database atGenBank provides a searchable tool for finding retroviral genome sequences, includingsuch information as the submitter and the original literature. The database iscomposed of retroviral sequences that have been described in the literature,and is continually being updated. In addition, the retroviral genome databaseat NCBI is a useful tool for the automated retrieval of similar genomes. Theretroviral genome sequence database at the Los Alamos National Laboratory providesa good source of information about retroviral genome structures and sequences.One of the strengths of the LAL database is the ability of users to searchhomology by both nucleic acid and protein sequences. Also included is theaccess to related sequence information, such as restriction maps, isolation methods,and experimental information (e.g., virus titer, antibody specificity, etc.). Along with theretroviral genome sequences (usually in FASTA format), the LAL Retroviral Genomesdatabase provides retrieval of genomic maps (e.g., protein or nucleic acid). Seehttp://www.hiv.lanl.gov/content/hiv-db/gene/retroviral_genomes/ for thecurrent release of the LAL Retroviral Genomes database. The RetroViral Genome Ontology is a set of terms to allow for the annotation and retrieval of information about retroviral genomes. See 827ec27edc