Tomato
Genetics
and Breeding Program
Tomato
Genetics
and Breeding Program
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Home Page for HCS806 - "Methods in BioInformatics for Plant Science"
Day 1
Downloading Custom Data sets (ppt)
Data: TA496 ESTs FASTA (warning: won't download)
TA496 ESTs text (warning: 76 Mb)
phtyphthora - tomato interaction FASTA
phytphthora - tomato interaction text
random tomato sequence text file
Day 2
Installing a UNIX emulator on your WINDOWS machine (ppt)
Day 3 - NOTE WE WILL MOVE THE CLASS TO GOURLEY HALL
SECOND FLOOR CONFERENCE ROOM (206).
Running Linux in Windows (ppt)
Day 4
Day 5
(Re-installation of Cygwin with PERL [use full installation])
Day 6
Introduction to PERL and BioPERL
(Includes installation of BioPERL)
Day 7
Sequence file
BioPERL Script to format sequence
Day 8
PERL script for parsing BLAST outputs
Sample BLAST output
Day 9
Protein data
SB6-94-4
SB7-15-13
SB7-15-13Pep4A
Parsing BLAST outputs
- Script modification
New Parsing PERL
script
Day 10
BLAST
Practice
PERL script for retrieving accessions identified in AraCyc
database
Day 11
Parsing BLAST (see day 8, practice, practice, practice)
Using the R statistical Package
Day 12
Finish GC content
excercise
Post-Class Survey
Discussion
References:
Mount, David W. 2004. Bioinformatics: Sequence and Genome Analysis, second edition. Cold Spring Harbor Laboratory Press, NY.
Danesh, A and Jan, M. 2001.
Mastering Linux. Red Hat Linux 7. Publisher's Edition. 2nd ed.
Barkakati, N and Wall, K. 2002. Red Hat Linux 7.2. Weekend crash course. Hungry
minds. P. 72-73, 85-86.
Holzner, S. 2001. Perl Black Book. Coriolis. 2nd edition.
Schwartz, R. and Phoenix, T. 2001.
Learning Perl. O'Reilly & Associates, Inc. Third edition.
Tisdall, J. 2003. Mastering
Perl for Bioinformatics. O'Reilly & Associates, Inc.First ed.
Wall, L., Christiansen, T. and Orwant, J. 2000. Programming Perl, 3rd Edition. O'Reilly Media, Inc
OhioLink allows OSU computers to access O'Reilly texts online: PERL on line