Databases

From Informatics

Contents 1 Database Inventory 1.1 BLAST 1.2 GeneTraffic 1.3 Geneways 1.4 PEP 1.5 CellCycleDB 1.6 ER-GolgiDB 1.7 LOC3D 1.8 LOChom 1.9 LOCkey 1.10 LOCtarget 1.11 NLSdb 1.12 NMP-db 1.13 Epitome 1.14 DSSPcontDB 1.15 HMAP 1.16 PrISM 1.17 SCOP 1.18 PDB

Database Inventory

Facilities hosting databases :  

(1) Genome Center http://genome4.cpmc.columbia.edu/

(2) Institute for Cancer Genetics - http://icg.cpmc.columbia.edu/default.htm

(3) C2B2 (Center for Computational Biology and Bioinformatics) - https://www.c2b2.columbia.edu/page.php?pageid=22

BLAST

• Available to all users within the GCG
• SSH to adtera.cu-genome.org, then login to adsolaris from there
  • Example: adgate> ssh adsolaris
  • You will then be given a login prompt on the adsolaris machine
• Command User Interface
• Flat-file database (FASTA-formatted files)
• Homology - to compare and find similar sequences using the BLAST engine
• BLAST Details

GeneTraffic

• Available to all labs within the GCG
• Web Interface
• PostgreSQL 7.1 relational database
• GeneTraffic
• Serves as a microarray database storage and analysis tool
• GeneTraffic Details

Geneways

• Available to anyone
• Rzhetsky lab
• Web interface
• Geneways
• Oracle 9i (Release 2) and indexed flat-files
• Geneways is a system for automatically extracting, analyzing, visualizing and integrating molecular pathway data from research literature
• Geneways Details

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PEP

• Database of Prediction for Entire Proteomes
• 413,630 proteins analyzed
• 105 organisms/proteomes analyzed
• Available to anyone
• Rost lab
• Web interface
• PEP
• PEP Details

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CellCycleDB

• Predict involvement in Cell Cycle control
• 599 protein entries
• Available to anyone
• Rost lab
• Web interface and can be queried using SRS (Sequence Retrieval System)
• CellCycleDB
• CellCycleDB catalogues proteins involved in the Cell Cycle Control Process through homology transfer from experimental annotations
• CellCycleDB Details

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ER-GolgiDB

• DataBase of predicted Endoplasmic Reticulum and Golgi Apparatus localization
• 11,990 protein entries
• Available to anyone
• Rost lab
• Web interface
• ER-GolgiDB
• ER and Golgi localization is predicted using the explicit "Accuracy versus Scaled HSSP distance" curves for each localization.
• ER-GolgiDB Details

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LOC3D

• Database of predicted subcellular LOCalization for eukaryotic 3D-PDB chains
• 8,795 PDB chains
• Available to anyone
• Rost lab
• Web Interface
• LOC3d
• LOC3d Details

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LOChom

• Database of predicted subcellular LOCalization based on sequence homology
• 54,876 homolog entries
• Available to anyone
• Rost lab
• Web Interface
• LOChom
• LOChom Details

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LOCkey

• database of predicted subcellular LOCalization for entire proteomes
• 19,948 protein entries
• Available to anyone
• Rost lab
• Web Interface
• LOCkey
• LOCkey Details

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LOCtarget

• database of predicted subcellular LOCalization for structural genomics targets
• 49,917 targets
• Available to anyone
• Rost lab
• Web Interface
• LOCtarget
• LOCtarget Details

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NLSdb

• database of nuclear localization signals (NLSs) and of nuclear proteins targeted to the nucleus by NLS motifs
• 308 entries
• Available to anyone
• Rost lab
• Web Interface
• NLSdb
• NLSdb Details

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NMP-db

• database of Nuclear Matrix-Associated Proteins
• 400 protein entries
• Available to anyone
• Rost lab
• Web Interface
• NMP-db
• NMP-db Details

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Epitome

• a database of all known antigenic residues and the antibodies that interact with them
• 10,116 antigenic residues
• Available to anyone
• Rost lab
• Web Interface
• Epitome
• Epitome Details

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DSSPcontDB

• holds PDB structure information for the DSSPcont program, which automates protein secondary structure assignment
• 42,082 protein structures
• Available to anyone
• Rost lab
• Web Interface
• DSSPcont
• DSSPcontDB Details

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=== ADOMETA === ADoption of Orphan METabolic Activities

• ADoption of Orphan METabolic Activities
• Available to anyone
• Vitkup lab
• Web Interface
• ADOMETA
• ADOMETA Details

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HMAP

• Hybrid Multidimensional Alignment of Profiles
• for internal use
• Honig lab
• HMAP
• HMAP Details

PrISM

• Protein Informatics System for Modeling
• for internal use
• Honig lab
• PrISM
• PrISM Details

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SCOP

• Structural Classification of Proteins
• 27,599 PDB Entries
• for internal use
• Honig lab
• SCOP
• SCOP Details

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PDB

• Protein Data Bank
• 42,069 structure entries
• for internal use
• Honig lab
• /razor/0/databases/pdb
• PDB Details