BIOINFORMATICS LAB-PAGE
The following experiments are meant for the students in their first course in bioinformatics laboratory [good for BTL58 of VTU and similar courses].
1. BIBLIOGRAPHIC DATABASES
(a)articles: www.ncbi.nlm.nih.gov
(b)Books: www.ncbi.nlm.nih.gov
(c) Non-scientific books: www.amazon.com
2. SEQUENCE RETRIEVAL:
(a) DNA SEQUENCE:
(i) www.ncbi.nlm.nih.gov (ii) www.ebi.ac.uk
(b) PROTEIN SEQUENCE(PROSITE): www.expasy.org/prosite/
3.RESTRICTION MAPS:
(i) www.neb.com
4.FASTA/BLAST SEARCHES:
www.ncbi.nlm.nih.gov/BLAST/
5.PAIRWISE ALIGNMENT:
www.ebi.ac.uk
6.MULTIPLE ALIGNMENT:
www.ebi.ac.uk
7. PROTEIN STRUCTURE PREDICTION:
(a) http://alexander.compbio.ucsf.edu/~nomi/nnpredict.html
(b) http://fasta.bioch.virginia.edu/
(c) Ramachandran Plot Server:
http://www.cmbi.kun.nl/swift/servers/modrama-submit.html
(d) ab initio models:
http://www.bioinfo.rpi.edu/~bystrc/hmmstr/server.php
8. HYDROPATHY PROFILE: http://fasta.bioch.virginia.edu/
9. PRIMER DESIGN:
http://seq.yeastgenome.org/cgi-bin/web-primer
http://frodo.wi.mit.edu/
10. GENE IDENTIFICATION:
www.ebi.ac.uk/genemark/ Then follow the link
http://genes.mit.edu Then click on Genscan
11. PATTERN SEARCHING (PROSITE/DALI):
(i) www.expasy.org/prosite/) http://bioweb.pasteur.fr) www.ebi.ac.uk/DALI/
12.PATTERN SEARCHING (NUCLEOTIDES):
(i) http://bioweb.pasteur.fr
13. VISUALIZATION OF 3-D STRUCTURES (RASMOL):
www.rcsb.org/pdb
(ii
(iii
14.SUPERPOSITION USING 'CHIMERA':
www.rbvi.ucsf.edu/chimera/
15.USING 'MOLPROBITY':
http://kinemage.biochem.duke.edu
16. OTHERS:
https://cbiores.com/molecular-docking-tutorial
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1. The experiments are easy; could be conducted just with an internet connection (even on rent) ---- essentially a prototype of my e-laboratory. You are welcome to send me e-mail for details.
2. SG thanks all his Vth Semester students (SIET2009BT) at the Shridevi Institute of Engineering and Technology (Tumkur, Karnataka) for helping him check lot of sites.
3. SG was paid by the SIET for teaching at the college.
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SG,
Nov. 17, 2007.
