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Related Subjects
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This category includes brief overview of all related subjects.
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Defining BioInformatics
[7]
In this section we tried to briefly explain what bioinformatics is ?
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Unviersities
[30]
This contains information about universities that are offering bioinformatics degree programs.
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Resources
[24]
Contains information about bioinformatics resources including databases, tools and techniques.
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Algorithms
[31]
This category includes some of the basic algorithms that are usually used by bioinformaticians.
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Home » 2011 » August » 11 » Tools For Protein Function Assignment
8:54 PM Tools For Protein Function Assignment |
Tools for protein function assignment
- Scan or search for patterns, motifs, profiles, domains, families
- ScanProsite (Scan a protein sequence against PROSITE pattern database at ExPASy, CH)
- PROSCAN (Scan a protein sequence against PROSITE pattern database allowing mismatches at PBIL, Lyon, Fr)
- PPSearch (Scan a protein sequence against PROSITE pattern database with graphical output at EBI, UK)
- PFSCAN (Scan protein against different profile databases at ISREC; also searches PROSITE and Pfam patterns)
- FingerPRINTScan (Scan a protein sequence against protein motif fingerprints database PRINTS)
- BLOCKS Search (Scan a protein against BLOCKS database; also searches PRINTS)
- eMOTIF-Scan (Scan for motifs that describe protein families or superfamilies at Stanford University, USA)
- Scansite (Prediction of protein signaling sequence motifs at MIT, Cambridge, USA)
- MEME (Multiple EM for Motive Elicitation: Motive discovery at San Diego Supercomputer Centre, SDSC, Ca, USA)
- eMotif-maker (Build motifs that describe protein families or superfamilies at Stanford University, USA)
- Meta-MEME (Buid motif at San Diego Supercomputer Centre, SDSC, Ca, USA)
- CDART (Conserved Domain Architecture Retrieval Tool at NCBI, USA)
- SearchPfam at Wustl or EBI (Search a protein against Pfam domain/family database)
- InterProScan (Search a protein against the integrated protein domains and functional sites database InterPro at EBI, UK)
- CD-Search (Search a protein against conserved domain database CDD with RPS-BLAST at NCBI, USA)
- COGnitor (Search a protein agains the COG database at NCBI)
- iProClass Search (Search a protein against PIR's integrated protein class database at Georgetown University, USA)
- SMART (Simple Modular Architecture Research Tool at EMBL; also searches Pfam)
- PROCAT (Search a protein structure agains the PROCAT database of 3D enzyme active site templates)
- ConSurf (Identification of functional regions in proteins by surface-mapping of phylogenetic information at Tel Aviv University, Israel)
- ProDom (Automatically generated protein domain database at Toulouse, Fr)
- Modules (Mobile protein domains database at EMBL)
- SBASE (Protein domain library at ICGEB, Trieste, It)
- HSSP (Database of homology-derived structures and sequences of proteins at EBI)
- 3Motif (Find protein (domain)s with defined 3D motifs at Stanford University, USA (runs only with Chime plugin))
- eMATRIX Search (Function prediction by sequence analysis using minimal-risk scoring matrices at Stanford University, USA)
- GeneQuiz (Automated analysis of protein sequences at EMBL)
- Search, computation and analysis of pathways
- KEGG (Search and computation tools at KEGG pathway database, Kyoto, Jp)
- aMAZE (Query tools for metabolic and signal transduction pathway analysis at ULB, Belgium)
- Protein-protein interactions
- DIP (Search Database of Interacting Proteins at UCLA, USA)
- PreBIND (Locate biomolecular interaction information in the scientific literature at the Samuel Lunenfeld Research Institute, Canada)
- BIND (Biomolecular Interaction Network Database at the Samuel Lunenfeld Research Institute, Canada )
- BINDBLAST (Search BIND database with BLAST)
- MINT (Molecular INTeraction database at Rome University, It)
- GRID (General Repository of Interaction Datasets at the Samuel Lunenfeld Research Institute, Canada)
- PPI viewer (Mammalian protein-protein interaction database and viewer at RIKEN, Japan)
- STRING (database of predicted functional associations among genes/proteins at the EMBL)
- InterPrets (Interaction prediction through structure at the EMBL)
- Protein Annotation
- PAA (Protein Annotator's Assistant at EBI, UK)
- AAT (Analysis and Annotation Tool for finding genes in genomic sequences at Michigan Tech, USA)
- Artemis (Free (large-) DNA sequence viewer and annotation tool at the Sanger Institute, UK)
- Gene Ontology tools (Universal function annotation vocabulary by the Gene Ontology Consortium)
- Automatic alert for related new sequence
- PubCrawler (Automated alerting service that scans daily updates to PubMed and GenBank databases at Trinity College Dublin, Ireland)
- Swiss-Shop (Automatically receive alerts upon new submissions of related protein sequences)
- New microbial Genomes Notification (Receive notifications by e-mail about new complete genomes in GenBank)
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