Allergen Atlas: a comprehensive knowledge center and analysis resource for allergen information
A variety of specialist databases have been developed to facilitate the study of allergens. However, these databases either contain different subsets of allergen data or are deficient in tools for assessing potential allergenicity of proteins. Here, we describe Allergen Atlas, a comprehensive reposi...
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| Veröffentlicht in: | Bioinformatics 2009-04, Vol.25 (7), p.979-980 |
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| creator | Tong, Joo Chuan Lim, Shen Jean Muh, Hon Cheng Chew, Fook Tim Tammi, Martti T. |
| description | A variety of specialist databases have been developed to facilitate the study of allergens. However, these databases either contain different subsets of allergen data or are deficient in tools for assessing potential allergenicity of proteins. Here, we describe Allergen Atlas, a comprehensive repository of experimentally validated allergen sequences collected from in-house laboratory, online data submission, literature reports and all existing general-purpose and specialist databases. Each entry was manually verified, classified and hyperlinked to major databases including Swiss-Prot, Protein Data Bank (PDB), Gene Ontology (GO), Pfam and PubMed. The database is integrated with analysis tools that include: (i) keyword search, (ii) BLAST, (iii) position-specific iterative BLAST (PSI-BLAST), (iv) FAO/WHO criteria search, (v) graphical representation of allergen information network and (vi) online data submission. The latest version contains information of 1593 allergen sequences (496 IUIS allergens, 978 experimentally verified allergens and 119 new sequences), 56 IgE epitope sequences, 679 links to PDB structures and 155 links to Pfam domains. Availability: Allergen Atlas is freely available at http://tiger.dbs.nus.edu.sg/ATLAS/. Contact: martti@nus.edu.sg. |
| doi_str_mv | 10.1093/bioinformatics/btp077 |
| format | Article |
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However, these databases either contain different subsets of allergen data or are deficient in tools for assessing potential allergenicity of proteins. Here, we describe Allergen Atlas, a comprehensive repository of experimentally validated allergen sequences collected from in-house laboratory, online data submission, literature reports and all existing general-purpose and specialist databases. Each entry was manually verified, classified and hyperlinked to major databases including Swiss-Prot, Protein Data Bank (PDB), Gene Ontology (GO), Pfam and PubMed. The database is integrated with analysis tools that include: (i) keyword search, (ii) BLAST, (iii) position-specific iterative BLAST (PSI-BLAST), (iv) FAO/WHO criteria search, (v) graphical representation of allergen information network and (vi) online data submission. The latest version contains information of 1593 allergen sequences (496 IUIS allergens, 978 experimentally verified allergens and 119 new sequences), 56 IgE epitope sequences, 679 links to PDB structures and 155 links to Pfam domains. Availability: Allergen Atlas is freely available at http://tiger.dbs.nus.edu.sg/ATLAS/. Contact: martti@nus.edu.sg.</description><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1460-2059</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/btp077</identifier><identifier>PMID: 19213741</identifier><identifier>CODEN: BOINFP</identifier><language>eng</language><publisher>Oxford: Oxford University Press</publisher><subject>Allergens - chemistry ; Applications Note ; Biological and medical sciences ; Computational Biology ; Databases, Protein ; Fundamental and applied biological sciences. Psychology ; General aspects ; Information Storage and Retrieval ; Internet ; Mathematics in biology. 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However, these databases either contain different subsets of allergen data or are deficient in tools for assessing potential allergenicity of proteins. Here, we describe Allergen Atlas, a comprehensive repository of experimentally validated allergen sequences collected from in-house laboratory, online data submission, literature reports and all existing general-purpose and specialist databases. Each entry was manually verified, classified and hyperlinked to major databases including Swiss-Prot, Protein Data Bank (PDB), Gene Ontology (GO), Pfam and PubMed. The database is integrated with analysis tools that include: (i) keyword search, (ii) BLAST, (iii) position-specific iterative BLAST (PSI-BLAST), (iv) FAO/WHO criteria search, (v) graphical representation of allergen information network and (vi) online data submission. The latest version contains information of 1593 allergen sequences (496 IUIS allergens, 978 experimentally verified allergens and 119 new sequences), 56 IgE epitope sequences, 679 links to PDB structures and 155 links to Pfam domains. Availability: Allergen Atlas is freely available at http://tiger.dbs.nus.edu.sg/ATLAS/. Contact: martti@nus.edu.sg.</description><subject>Allergens - chemistry</subject><subject>Applications Note</subject><subject>Biological and medical sciences</subject><subject>Computational Biology</subject><subject>Databases, Protein</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>General aspects</subject><subject>Information Storage and Retrieval</subject><subject>Internet</subject><subject>Mathematics in biology. Statistical analysis. Models. Metrology. 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Psychology</topic><topic>General aspects</topic><topic>Information Storage and Retrieval</topic><topic>Internet</topic><topic>Mathematics in biology. Statistical analysis. Models. Metrology. 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However, these databases either contain different subsets of allergen data or are deficient in tools for assessing potential allergenicity of proteins. Here, we describe Allergen Atlas, a comprehensive repository of experimentally validated allergen sequences collected from in-house laboratory, online data submission, literature reports and all existing general-purpose and specialist databases. Each entry was manually verified, classified and hyperlinked to major databases including Swiss-Prot, Protein Data Bank (PDB), Gene Ontology (GO), Pfam and PubMed. The database is integrated with analysis tools that include: (i) keyword search, (ii) BLAST, (iii) position-specific iterative BLAST (PSI-BLAST), (iv) FAO/WHO criteria search, (v) graphical representation of allergen information network and (vi) online data submission. The latest version contains information of 1593 allergen sequences (496 IUIS allergens, 978 experimentally verified allergens and 119 new sequences), 56 IgE epitope sequences, 679 links to PDB structures and 155 links to Pfam domains. Availability: Allergen Atlas is freely available at http://tiger.dbs.nus.edu.sg/ATLAS/. Contact: martti@nus.edu.sg.</abstract><cop>Oxford</cop><pub>Oxford University Press</pub><pmid>19213741</pmid><doi>10.1093/bioinformatics/btp077</doi><tpages>2</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Allergens - chemistry Applications Note Biological and medical sciences Computational Biology Databases, Protein Fundamental and applied biological sciences. Psychology General aspects Information Storage and Retrieval Internet Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Proteins - chemistry Proteins - immunology |
| title | Allergen Atlas: a comprehensive knowledge center and analysis resource for allergen information |
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