Bioinformatics Syllabus : www.karunya.edu University

[mariammal]

BI216 BIOINFORMATICS NETWORKS AND APPLICATIONS
Credit: 4:0:0

Unit I Introduction to Bioinformatics
Scope of Bioinformatics – Elementary commands and Protocols, ftp, telnet, http. Printer on information theory. Databanks – nucleotide databanks – Genbank, NCBI, EMBL, DDBJ – protein databanks – sequence databanks – PIR, SWISSPROT, TrEMBL _ structural databases – PDB, SCOP, CATH, SSEP, CADB, Pfam and GDB.

http://www.karunya.edu/academics/syllabus.html
http://www.karunya.edu/academics/syl...nformatics.pdf

Unit II : Sequence Alignment and Dynamic Programming
Introduction – Strings – Edit distance two strings – string similarity local alignment -gaps – Parametric sequence alignments – suboptimal alignments – multiple alignment – common multiple alignment methods.

Unit III : Sequence Databases and Their Uses
Introduction to databases – database search – Algorithms issues in database search – sequence database search – FASTA – BLAST – Amino acid substitution matrices PAM250 and BLOSUM62. GCG Sequence Analysis(Basic concepts only)

Unit IV : Evolutionary Trees and Phylogeny
Ultrasonic trees – parsimony – Ultrametric problem – Perfect phylogeny – Phylogenetic alignment – connection between multiple alignment and tree construction.

Unit V : Special Topics in Bioinformatics
DNA Mapping and sequencing – Map alignment – Large scale sequencing and alignment – Shotgun – DNA sequencing – Sequence assembly – Gene predictions – Molecular predictions with DNA strings.

Text Book :
1. T.K.Attwood & D.Parry-Smith, Introduction to Bioinformatics, Pearson Education, 2001.
2. R.Durbin, R.Eddy, K.Anders and M.Graeme, Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Cambridge University Press, 1997

Reference Books :
1. Dan Gusfield, Algorithms On Strings Trees And Sequences, Cambridge University Press, 1997.
2. Lesk, Introduction to Bioinformatics, Oxford University Press, 2002.
3. Pennington, Proteomics from Protein Sequence to Function
4. Campell, Discovering Genomics, Proteomics and Bioinformatics
5. Baxevenis, Bioinformatics, John Wiley & Sons