3rd South East Asian Training Course on Bioinformatics Applied to Tropical Diseaes Sept 28-Oct 11, 2004, International Centre for Genetic Engineering and Biotechnology (ICGEB) New Delhi, India

Sequence Analysis - Raghava

- Lecture - Basics of Sequence alignments, scoring matrices: Global and local alignments

• seq_analysis_01_align_20041001.ppt
  • ShowAndTell Sync Presentation
• seq_analysis_01_align_20041001_2.ppt (after intermission)
  • ShowAndTell Sync Presentation

- BLAST Lecture - seq_analysis_02_align_scan_20041001.ppt -- extra material for BLAST (Self-Read)

- Local BLAST installation and interpretation of BLAST runs - DEMO

• Download blast-2.2.9-ia32-linux.tar.gz -- local copy of local BLAST program (for Linux)
  • The latest version is available online at: ftp://ftp.ncbi.nih.gov/blast/executables/
• Create a directory called "blast". [Hint: mkdir blast]
• Move blast-2.2.9-ia32-linux.tar.gz into this newly created blast directory [Hint: mv blast-2.2.9-ia32-linux.tar.gz blast/]
• Uncompress blast-2.2.9-ia32-linux.tar.gz [Hing: tar zxvf blast-2.2.9-ia32-linux.tar.gz]
• Read blast.txt file
  • cd data
  • ../formatdb -i humrep.fsa -p F -o T
• head -7 humrep.fsa > test.fsa
• ../blastall -p blastn -i test.fsa -d humrep.fsa -o output

Self Study Extra for sequence analysis

• align_mult_extra.ppt
• align_wm_extra.ppt

Last updated: Tuesday, October 5, 2004 5:34 (Delhi Time GMT+5:30)