Scribd
Upload
105 views

BIOT 206 - Lecture 1

This document provides an overview of bioinformatics resources for genomics, proteomics, and molecular modeling tools. It lists important biological databases, genomics tools for simple DNA sequence manipulation and analysis including pairwise and multiple sequence alignment tools. Proteomics tools described include sequence similarity searches, protein accession numbers, gel electrophoresis analysis, mass spectrometry, protein structure and function prediction. Finally, it provides tutorials for basic and advanced use of molecular modeling software.

Uploaded by

Kathmandu University - Department Of Biotechnology
Copyright
© Attribution Non-Commercial (BY-NC)
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd
105 views

BIOT 206 - Lecture 1

This document provides an overview of bioinformatics resources for genomics, proteomics, and molecular modeling tools. It lists important biological databases, genomics tools for simple DNA sequence manipulation and analysis including pairwise and multiple sequence alignment tools. Proteomics tools described include sequence similarity searches, protein accession numbers, gel electrophoresis analysis, mass spectrometry, protein structure and function prediction. Finally, it provides tutorials for basic and advanced use of molecular modeling software.

Uploaded by

Kathmandu University - Department Of Biotechnology
Copyright
© Attribution Non-Commercial (BY-NC)
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd
You are on page 1/ 3

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)

You might also like