BIOINFORMATICS RESOURCES

Genomics Tools | Proteomics Tools | Molecular Modeling Tools

Questions For Exam (Lab 1):

• DNA1
• DNA2
• DNA3
• Protein1
• Protein2

Some Important Biological Databases

• NCBI
• EMBL-EBI
• DDBJ
• RCSB Protein Data Bank
• ExPASy Proteomics Server
Biology Workbench for Molecular biologist & Biotechnologist
• SDSC Biology Workbench

Genomics Tools
Simple DNA sequence manipulation

• DownloadJambWand useSequence&Sequenceas templates

• DownloadJava
• DownloadBioinformatics Bookmark
• DownloadRasmol
• for Rasmol: Use .pdb file ofBovine Cytochrome (PDB ID - 1CYO)
• Rasmol Tutorials
• Protein file
• 1NHJ
• 1R50
• Phylip Links ==>phylipw,phylipwx,phylipwy,PHYLIP tutorial,Test
• RNA sequence
• MFOLD link
• phylip test
• RNA
Pairwise Sequence Similarity Tool

• http://www.ncbi.nlm.nih.gov/BLAST/
 • http://www.ebi.ac.uk/Tools/fasta33/
Multiple Sequence Alignment

• http://www.ebi.ac.uk/clustalw/ and use Sequence as template

Proteomics Tools
Sequence Similarity search with UniPort Knowledgebase

• http://www.ebi.ac.uk/MPsrch/and useSequenceas template

Accession no. of Proteins

• O93215
• O89290

Gelscape
• Example1
• Example2

Mass Spectrometry Lab. using MASCOT

• www.matrixscience.com
• Peptide Mass fingerprinting (PMFdata.txt)
• MS/MS (MSMS2.txt)
Protein Pattern and Profile Search

• InterProScan:http://www.ebi.ac.uk/InterProScanand useSequenceas template

Protein Secondary Structure Prediction

• PredictProtein:http://cubic.bioc.columbia.edu/predictprotein/
• PSIPRED:http://bioinf.cs.ucl.ac.uk/psipred/
Protein Tertiary Structure Prediction
• Homology Modelling
SWISS MODEL:http://swissmodel.expasy.org/
• Protein Threading
GenTHREADER:http://bioinf.cs.ucl.ac.uk/psipred/psiform.html

Molecular Modeling for Beginners

Basic Tutorial of DeepView
 • DownloadSwiss PDB Viewer
• Downloadtutorial(Open index.html)
• 1HEW.pdb
Advanced Tutorials

• DeepView Manual
• Loops database(Put it inside "_stuff_" directory)
• Advanced tutorial(Put it inside "_stuff_" directory and open index.html to use from text
folder)
• Deoxyhaemoglobin (3HHB.pdb)
• Oxyhaemoglobin (1HHO.pdb)
• Lactate dehydrogenase (1ldm.pdb)