| SARS | Severe Acute Respiratory Syndrome |
| CDS | coding sequences |
| ORFs | Open Reading Frames |
| SSS | Secondary Structural Sequence |
| TRS | Transcription Regulating Sequence |
| 5'UTR | 5' Untranslated Region |
| 3'UTR | 3' Untranslated Region |
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| RdRp | RNA-dependent RNA polymerase |
| pp1a | nonstructural polyprotein 1a |
| pp1b | nonstructural polyprotein 1b |
| S protein | Spike protein |
| E protein | Envelop protein |
| M protein | Membrane protein |
| N protein | Nucleocapsid protein |
| PUP | Putative Uncharacterized Protein |
| s protein | structural protein |
| n-s protein | non-structural protein |
| gpro | glycoprotein |
| rep | replicase |
| HE | haemuggltinin-esteras |
| Hel | helicase |
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| CoV | coronavirus |
| HCoV | human coronavirus |
| SARS-CoV | SARS coronavirus |
| BCoV | bovine coronavirus |
| TGEV | porcine transmissible gastroenteritis virus |
| MHV | mouse heptitis virus |
| IBV | avian infectious branchitsi virus |
| TBV | turkey bluecomb virus |
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| RNA SSS | RNA secondary structural sequences |
| H | hairpin loop |
| D | in-Double strand in the 5'end ( upstream ) |
| d | out-double strand in the 3'end ( downstream ) |
| I | in-Internal loop in the 5'end ( upstream ) |
| i | out-internal loop the 3'end ( downstream ) |
| B | in-Bulge loop in the 5'end ( upstream ) |
| b | out-bulge loop in the 3'end ( downstream ) |
| M | Multibranch loop |
| F | Free unpaired nucleotides |
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| DNA | Deoxyribonucleic Acid |
| RNA | Ribonucleic Acid |
| mRNA | messenger RNA |
| rRNA | ribosomal RNA |
| tRNA | transfer RNA |
| ssRNA | single-strand RNA |
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| bp | base pair (in case of double-stranded DNA/RNA ) |
| kb | kilo bases (1,000 b) |
| kbp | kilo base pairs (1,000 bp) |
| Mbp | mega base pairs (1,000,000 bp) |
| Gbp | giga base pairs (1,000,000,000 bp) |
| nt | nucleotide (in case of single-stranded DNA/RNA ) |
| 90 nt | 90 nucleotides |
| knt | kilo nucleotides (1,000 nt) |
| Mnt | mega nucleotides (1,000,000 nt) |
| Gnt | giga nucleotides (1,000,000,000 nt) |
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| SRS | Sequence Retrieval System |
| DB | DATABASE / DATABANK |
| NMR | Nuclear Magnetic Resonance |
| InBase | a database of inteins |
| ReBase | DataBase of Restriction endonucleases and their target sites |
| TRANSFAC | a database of TRANScription FACtors |
| Sentra | a database of signal transduction proteins |
| ESTs | Expressed Sequence Tags |
| GOLD | the Genomes OnLine Databases |
| OMIM | Online Mendelian Inheritance in Man |
| RCSB | Research Collaboratory for Structural Bioinformatics |
| PIR | Protein Information Resource |
| KEGG | Kyoto Encyclopedia of Genes and Genomes |
| MSD | Macromolecular Structure Database |
| MGD | Mouse Genome Database |
| MMDB | Molecular Modeling Database |
| DIP | the Database of Interacting Protein |
| BIND | Bimolecular Interaction Network Database |
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| URL | Uniform Resource Locator |
| WWW | World wide Web |
| NCBI | National Center for Biotechnology Information |
| EMBL | European Molecular Biology Laboratory |
| DDBJ | DNA DataBank of Japan |
| PDB | Protein Data Bank |
| NIH | National Institute of Health |
| WHO | World Health Organization |
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