Bioinformatics

Primary Databases: EMBL/GenBank/DDBJ, PIR, Swiss-Prot

• EMBL
• NCBI
• ExPASy (Bioinformatics Resource Portal)
• Genome project
• E. coli whole genome sequence
• Gene function
• Genome browser
• Individual metabolic pathways
• Full metabolic maps
• E. coli K-12 Regulon DB
• Protein Data Bank (PDB)
• Multiple Sequence Alignment (Clustal Omega, ClustalW2, ClustalW)

Motif Databases: BLOCKS, Prosite, Pfam, ProDom, SMART

• MOTIF Scan
• Pfam

Others

• Restriction site analysis; RestrictionMapper
• Sequence Conversion Tool; Reverse complement
• Translation into protein; with DNA sequence
• RNAstructure:
• BioCyc data collection
• UTR Designer, UTR Library Designer, RBS Calculator, RBSDesigner
• ChemSpider/The free chemical database
• Profiling of E. coli chromosome (essential/non essential genes)
• The Coli Genetic Stock Center (mutants)
• Genomic tRNA Database
• Promoter/terminator finder

Chemicals

• ChemSpider/The free chemical database
• Sigma Aldrich/Chemicals price

RNA

• Codon table
• RNA analysis

Protein

1. Rational design of temperature-sensitive mutants

Protein Structure Analysis :

Visible programs

•COOT -- Model building (CCP4)

•PyMOL -- High visible program (need a license)

◦CAVER -- Display cavity

•MOLSCRIPT

•Raster3D

•CCP4MG (CCP4)

•XtalView -- Model building

•O -- Model building

•MIFit -- Model building

•LIGPLOT -- Display interaction of ligand (2D)

•RasMol -- Basic visible program

•Jmol -- an open-source Java viewer for chemical structures in 3D

Analysis programs :

Data process(integrate＋scaling)

•IDIFFDISP -- Diffraction image display (CCP4)

•MOSFLM

•iMOSFLM -- Totally data process interface (CCP4)

•HKL2000 (DENZO) (need a license)

•XDS

•XIA2 -- Automatic data process

•POSTREF -- Post-refinement (CCP4)

Molecular replacement (MR)

•MrBUMP -- Automatic molecular replacement

•BALBES -- Automatic molecular replacement

•MOLREP

Phasing

•SHELX

•SOLVE/RESOLVE -- Phasing & improvement

•SHARP

•HKL2MAP

Model building

•ARP/wARP -- Automatic model building (need a license)

•BUCCANEER -- Automatic model building

Refinement

•CNS

•LAFIRE -- Automatic refinement

•SHELXL

•Refmac5

Validation

•RAMPAGE (CCP4)

•PROCHECK (CCP4)

•MolProbity

•SFCHECK

•DSSP -- Assign of secondary structure

•WHAT_CHECK

•PDB Validation Suite

User interface

•CCP4i

•PHENIX

Protein structure package

•CCP4 -- Totally programs

•PHENIX (including PHASER, RESOLVE)

Etc.

•Calculation ; ◦CROSSEC --Calculate anomalous scattering factor(CCP4)

•File conversion ; ◦FFT -- Create an electron density map from MTZ file (CCP4)

◦MAKECIF -- Create a CIF file from PDB file (CCP4)

•Sequence alignment ; ◦ClustalW

◦FASTA

•Etc. ; ◦EMBOSS

◦RAVE

◦FIT2D

◦MLFSOM -- Output of diffraction image from PDB file

◦PDB_EXTRACT -- Extract from log file

◦PDB_EXTRACT_SF -- Create mmCIF file from structure Factor file

◦DIFF2JPEG -- Create JPEG file from diffraction image (CCP4)

◦BAUBLES -- Trimming HTML file form log file of CCP4

◦ROSETTA -- Prediction

Molecular dynamics(MD)

•AMBER -- MD

•CHARMM -- MD

•GLOMACS -- Free MD program

Company

• Sigma Aldrich/Chemicals price
• BioCNS/Fermentor
• KoBioTech/Fermentor
• Fermentec/Fermentor
• Agilent Technologies/Genomics
• 서린바이오사이언스 (Seoulin Bioscience)
• ebiogen (DNA microarray, NGS, research plan)

Pathway Database

• Biofuels
• BioCyc data collection
• Kyoto Encyclopedia of Genes and Genomes(KEGG)
• METACyc (a member of the BioCyc database collection)
• Pathway Hunter Tool (PHT)

Transcriptome Databases:SAGE, ArrayExpress, GEO

• ArrayExpress
• Genome/Transcriptome/Proteome(kobio)

Hydrophobicity

• Kyte-Doolittle plot
• Phobius

Phylogenetic analysis

• MEGA

Riboswitch

• Aptagen - aptamer catalog
• Aptamer Base - Quick Search Aptamer Base's SELEX experiments by Target

Useful Websites

• Baneyx BioNano Lab