Algorithms and tools suitable for analysis of platelet proteome data
| Name . | Description . | Source . |
|---|---|---|
| UniProt | Curated database with linked information sources, retrieval of fasta sequences, etc | http://www.uniprot.org/33 |
| Protein identifier cross reference service (PICR) | Cross-reference algorithm for accession exchange between different formats (eg, NCBI vs Swiss-Prot or gene name vs Swiss-Prot accession) | http://www.ebi.ac.uk/Tools/picr/34 |
| Expasy | Proteomics server for various prediction and sequence analysis programs (eg, prediction of phosphorylation and glycosylation sites, TMDs, import sequences, domains) | http://www.expasy.org/tools/ |
| TMHMM 2.0 | Prediction of transmembrane domains | http://www.cbs.dtu.dk/services/TMHMM/ |
| Simple Modular Architechture Research Tool (SMART) | Prediction and annotation of protein domains, internal links to PFAM | http://smart.embl-heidelberg.de/smart/batch.pl35 |
| ProtFun 2.2 | Ab initio prediction of protein function, enzymatic properties and possible gene ontology, ab initio predictions of protein function from sequence. | http://www.cbs.dtu.dk/services/ProtFun/36 |
| STRING | STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations | http://string.embl.de/37 |
| Unified Human Interactome (UniHI) | Interaction network prediction | http://theoderich.fb3.mdc-berlin.de:8080/unihi/home38 |
| GoMiner | Evaluation of gene ontology classification for large scale data | http://discover.nci.nih.gov/gominer/39 |
| Ontologizer | Evaluation of gene ontology classification for large scale data, comparison between datasets | http://compbio.charite.de/index.php/ontologizer2.html |
| Bioinformatic Harvester III | Harvester crawls and cross-links the following bioinformatic sites: 4DXp, AceView, BLAST, Biocompare, CDART, CDD, ensEMBL, Entrez, FishMap, Galaxy, UCSC GenomeBrowser, gfp-cDNA, Google-Scholar, gopubmed, Harvester42, H-Inv, HomoloGene, iHOP, IPI, MapView, MGI, MINT, Mitocheck, OMIM, PolyMeta, PSORT II, RGD, SMART, SOSUI SOURCE, STRING, TAIR, Unigene, UniprotKB, Wikipedia, WikiProtein | http://harvester.fzk.de/harvester/40 |
| Reactome (including SkyPainter) | Curated knowledgebase of biologic pathways | http://www.reactome.org41 |
| KEGG PATHWAY database | Collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks (also accessible via STRING) | http://www.genome.jp/kegg/pathway.html42 |
| iHOP | Hyperlinked information about proteins | http://www.ihop-net.org/UniPub/iHOP/43 |
| Name . | Description . | Source . |
|---|---|---|
| UniProt | Curated database with linked information sources, retrieval of fasta sequences, etc | http://www.uniprot.org/33 |
| Protein identifier cross reference service (PICR) | Cross-reference algorithm for accession exchange between different formats (eg, NCBI vs Swiss-Prot or gene name vs Swiss-Prot accession) | http://www.ebi.ac.uk/Tools/picr/34 |
| Expasy | Proteomics server for various prediction and sequence analysis programs (eg, prediction of phosphorylation and glycosylation sites, TMDs, import sequences, domains) | http://www.expasy.org/tools/ |
| TMHMM 2.0 | Prediction of transmembrane domains | http://www.cbs.dtu.dk/services/TMHMM/ |
| Simple Modular Architechture Research Tool (SMART) | Prediction and annotation of protein domains, internal links to PFAM | http://smart.embl-heidelberg.de/smart/batch.pl35 |
| ProtFun 2.2 | Ab initio prediction of protein function, enzymatic properties and possible gene ontology, ab initio predictions of protein function from sequence. | http://www.cbs.dtu.dk/services/ProtFun/36 |
| STRING | STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations | http://string.embl.de/37 |
| Unified Human Interactome (UniHI) | Interaction network prediction | http://theoderich.fb3.mdc-berlin.de:8080/unihi/home38 |
| GoMiner | Evaluation of gene ontology classification for large scale data | http://discover.nci.nih.gov/gominer/39 |
| Ontologizer | Evaluation of gene ontology classification for large scale data, comparison between datasets | http://compbio.charite.de/index.php/ontologizer2.html |
| Bioinformatic Harvester III | Harvester crawls and cross-links the following bioinformatic sites: 4DXp, AceView, BLAST, Biocompare, CDART, CDD, ensEMBL, Entrez, FishMap, Galaxy, UCSC GenomeBrowser, gfp-cDNA, Google-Scholar, gopubmed, Harvester42, H-Inv, HomoloGene, iHOP, IPI, MapView, MGI, MINT, Mitocheck, OMIM, PolyMeta, PSORT II, RGD, SMART, SOSUI SOURCE, STRING, TAIR, Unigene, UniprotKB, Wikipedia, WikiProtein | http://harvester.fzk.de/harvester/40 |
| Reactome (including SkyPainter) | Curated knowledgebase of biologic pathways | http://www.reactome.org41 |
| KEGG PATHWAY database | Collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks (also accessible via STRING) | http://www.genome.jp/kegg/pathway.html42 |
| iHOP | Hyperlinked information about proteins | http://www.ihop-net.org/UniPub/iHOP/43 |