PairsDB atlas of protein sequence space.
Sequence similarity/database searching is a cornerstone of molecular biology. PairsDB is a database intended to make exploring protein sequences and their similarity relationships quick and easy. Behind PairsDB is a comprehensive collection of protein sequences and BLAST and PSI-BLAST alignments bet...
| Main Authors: | , , , , , |
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| Format: | Journal article |
| Language: | English |
| Published: |
2008
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| _version_ | 1826305629021536256 |
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| author | Heger, A Korpelainen, E Hupponen, T Mattila, K Ollikainen, V Holm, L |
| author_facet | Heger, A Korpelainen, E Hupponen, T Mattila, K Ollikainen, V Holm, L |
| author_sort | Heger, A |
| collection | OXFORD |
| description | Sequence similarity/database searching is a cornerstone of molecular biology. PairsDB is a database intended to make exploring protein sequences and their similarity relationships quick and easy. Behind PairsDB is a comprehensive collection of protein sequences and BLAST and PSI-BLAST alignments between them. Instead of running BLAST or PSI-BLAST individually on each request, results are retrieved instantaneously from a database of pre-computed alignments. Filtering options allow you to find a set of sequences satisfying a set of criteria-for example, all human proteins with solved structure and without transmembrane segments. PairsDB is continually updated and covers all sequences in Uniprot. The data is stored in a MySQL relational database. Data files will be made available for download at ftp://nic.funet.fi/pub/sci/molbio. PairsDB can also be accessed interactively at http://pairsdb.csc.fi. PairsDB data is a valuable platform to build various downstream automated analysis pipelines. For example, the graph of all-against-all similarity relationships is the starting point for clustering protein families, delineating domains, improving alignment accuracy by consistency measures, and defining orthologous genes. Moreover, query-anchored stacked sequence alignments, profiles and consensus sequences are useful in studies of sequence conservation patterns for clues about possible functional sites. |
| first_indexed | 2024-03-07T06:35:44Z |
| format | Journal article |
| id | oxford-uuid:f79013eb-2a39-4699-b93a-3998725b74f6 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T06:35:44Z |
| publishDate | 2008 |
| record_format | dspace |
| spelling | oxford-uuid:f79013eb-2a39-4699-b93a-3998725b74f62022-03-27T12:43:56ZPairsDB atlas of protein sequence space.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:f79013eb-2a39-4699-b93a-3998725b74f6EnglishSymplectic Elements at Oxford2008Heger, AKorpelainen, EHupponen, TMattila, KOllikainen, VHolm, LSequence similarity/database searching is a cornerstone of molecular biology. PairsDB is a database intended to make exploring protein sequences and their similarity relationships quick and easy. Behind PairsDB is a comprehensive collection of protein sequences and BLAST and PSI-BLAST alignments between them. Instead of running BLAST or PSI-BLAST individually on each request, results are retrieved instantaneously from a database of pre-computed alignments. Filtering options allow you to find a set of sequences satisfying a set of criteria-for example, all human proteins with solved structure and without transmembrane segments. PairsDB is continually updated and covers all sequences in Uniprot. The data is stored in a MySQL relational database. Data files will be made available for download at ftp://nic.funet.fi/pub/sci/molbio. PairsDB can also be accessed interactively at http://pairsdb.csc.fi. PairsDB data is a valuable platform to build various downstream automated analysis pipelines. For example, the graph of all-against-all similarity relationships is the starting point for clustering protein families, delineating domains, improving alignment accuracy by consistency measures, and defining orthologous genes. Moreover, query-anchored stacked sequence alignments, profiles and consensus sequences are useful in studies of sequence conservation patterns for clues about possible functional sites. |
| spellingShingle | Heger, A Korpelainen, E Hupponen, T Mattila, K Ollikainen, V Holm, L PairsDB atlas of protein sequence space. |
| title | PairsDB atlas of protein sequence space. |
| title_full | PairsDB atlas of protein sequence space. |
| title_fullStr | PairsDB atlas of protein sequence space. |
| title_full_unstemmed | PairsDB atlas of protein sequence space. |
| title_short | PairsDB atlas of protein sequence space. |
| title_sort | pairsdb atlas of protein sequence space |
| work_keys_str_mv | AT hegera pairsdbatlasofproteinsequencespace AT korpelainene pairsdbatlasofproteinsequencespace AT hupponent pairsdbatlasofproteinsequencespace AT mattilak pairsdbatlasofproteinsequencespace AT ollikainenv pairsdbatlasofproteinsequencespace AT holml pairsdbatlasofproteinsequencespace |