Difference between revisions of "Resource data"
From Bioinformatikpedia
(New page: == Disease info == * [http://www.hgmd.cf.ac.uk/docs/login.html HGMD] - "Human Gene Mutation Database", collects sequence and mutation information, links to other resources, e.g. OMIM * [ht...) |
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* [http://www.hgmd.cf.ac.uk/docs/login.html HGMD] - "Human Gene Mutation Database", collects sequence and mutation information, links to other resources, e.g. OMIM |
* [http://www.hgmd.cf.ac.uk/docs/login.html HGMD] - "Human Gene Mutation Database", collects sequence and mutation information, links to other resources, e.g. OMIM |
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* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim&TabCmd=Limits OMIM] - "Online Mendelian Inheritance in Man" maintained at NCBI, has many links to related data (gene, protein, literature, etc.) |
* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim&TabCmd=Limits OMIM] - "Online Mendelian Inheritance in Man" maintained at NCBI, has many links to related data (gene, protein, literature, etc.) |
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| + | * [http://www.genome.jp/kegg/disease/ KEGG Disease] - The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations of the KEGG pathways (see Pathway section). |
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== Protein sequence info == |
== Protein sequence info == |
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* [http://www.uniprot.org/ Uniprot] - central sequence repository (mainly used in Europe) with data from Swissprot and Trembl (and many links to related data) |
* [http://www.uniprot.org/ Uniprot] - central sequence repository (mainly used in Europe) with data from Swissprot and Trembl (and many links to related data) |
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* [http://www.ncbi.nlm.nih.gov/protein NCBI Protein] - central protein sequence search interface of NCBI, includes data from GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB |
* [http://www.ncbi.nlm.nih.gov/protein NCBI Protein] - central protein sequence search interface of NCBI, includes data from GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB |
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| + | === Local data === |
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| + | * big: all sequences from Swissprot, Trembl and PDB (path: <code>/mnt/project/pracstrucfunc12/data/big/big*</code>) |
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| + | * big_80: cluster representatives of big clustered at 80% sequence identity using CD_HIT (path: <code>/mnt/project/pracstrucfunc12/data/big/big_80*</code>) |
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| + | * uniprot for hhblits: <code>/mnt/project/pracstrucfunc12/data/hhblits/uniprot20 </code> |
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| + | * SwissProt: /mnt/project/pracstrucfunc13/data/swissprot/uniprot_sprot (BLAST db, May 7, 2013) |
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| + | * PDB SEQRES: /mnt/project/pracstrucfunc13/data/pdb/pdb_seqres (BLAST db, May 7, 2013) |
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== Structure info == |
== Structure info == |
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* [http://www.ebi.ac.uk/pdbsum/ PDBsum] - structural annotations of PDB structures (analysis of interactions between chains and with small molecule ligands) |
* [http://www.ebi.ac.uk/pdbsum/ PDBsum] - structural annotations of PDB structures (analysis of interactions between chains and with small molecule ligands) |
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* [http://srs3d.org/ SRS 3D] - quick access to related structures (based on HSSP): search for Uniprot identifier of your protein -> get a list of related structures; click on a structure -> view the sequence aligned to the related structure |
* [http://srs3d.org/ SRS 3D] - quick access to related structures (based on HSSP): search for Uniprot identifier of your protein -> get a list of related structures; click on a structure -> view the sequence aligned to the related structure |
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| + | == Pathway info == |
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| + | * [http://www.genome.jp/kegg/kegg2.html KEGG] - "Kyoto Encyclopedia of Genes and Genomes" collects maps of metabolic pathways etc. |
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| + | * [http://metacyc.org/ MetaCyc] - database of nonredundant, experimentally elucidated metabolic pathways (from literature), contains pathways involved in both primary [def] and secondary [def] metabolism, as well as associated compounds, enzymes, and genes. |
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Latest revision as of 21:27, 27 May 2013
Disease info
- HGMD - "Human Gene Mutation Database", collects sequence and mutation information, links to other resources, e.g. OMIM
- OMIM - "Online Mendelian Inheritance in Man" maintained at NCBI, has many links to related data (gene, protein, literature, etc.)
- KEGG Disease - The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations of the KEGG pathways (see Pathway section).
Protein sequence info
- Uniprot - central sequence repository (mainly used in Europe) with data from Swissprot and Trembl (and many links to related data)
- NCBI Protein - central protein sequence search interface of NCBI, includes data from GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB
Local data
- big: all sequences from Swissprot, Trembl and PDB (path:
/mnt/project/pracstrucfunc12/data/big/big*) - big_80: cluster representatives of big clustered at 80% sequence identity using CD_HIT (path:
/mnt/project/pracstrucfunc12/data/big/big_80*) - uniprot for hhblits:
/mnt/project/pracstrucfunc12/data/hhblits/uniprot20 - SwissProt: /mnt/project/pracstrucfunc13/data/swissprot/uniprot_sprot (BLAST db, May 7, 2013)
- PDB SEQRES: /mnt/project/pracstrucfunc13/data/pdb/pdb_seqres (BLAST db, May 7, 2013)
Structure info
- PDB - "Protein Data Bank", central repository for protein structures
- PDBsum - structural annotations of PDB structures (analysis of interactions between chains and with small molecule ligands)
- SRS 3D - quick access to related structures (based on HSSP): search for Uniprot identifier of your protein -> get a list of related structures; click on a structure -> view the sequence aligned to the related structure
Pathway info
- KEGG - "Kyoto Encyclopedia of Genes and Genomes" collects maps of metabolic pathways etc.
- MetaCyc - database of nonredundant, experimentally elucidated metabolic pathways (from literature), contains pathways involved in both primary [def] and secondary [def] metabolism, as well as associated compounds, enzymes, and genes.
