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FOSS Tools for Bioinformatics
Deepan Chakravarthy N
Svapas Innovations, Chennai.
codeshepherd AT yahoo DOT com
Bio-Nix
A linux Distro for Biotech people
Project Wiki Page
Built using Fedora Core 5 as base
YUM repository for Biotech related software
Please contribute. Join our Mailing List
Demo of Bio-Nix YUM repository.
Gromacs
Demo: Gromacs installation; MD simulation to set up a small peptide surrounded by water, and then run an energy-minimization
Gromacs Hello World Tutorial
$cp /usr/share/gromacs/tutor/speptide/* .
$echo 0 | pdb2gmx -f speptide.pdb -o speptide.gro -p speptide.top >& output.pdb2gmx
$editconf -f speptide.gro -o speptide.gro -d 0.5 >& output.genbox
Gromacs demo continued..
genbox -cp speptide.gro -cs -o speptide_b4em.gro -p speptide.top >>& output.genbox
$grompp -f em -c speptide_b4em -p speptide -o speptide_em >& output.grompp_em
$mdrun -nice 4 -s speptide_em -o speptide_em -c speptide_b4pr -v
Emboss
Demo: Emboss installation; Generate random nucleotide/protein sequence, play with it.
Emboss tutorials
wossname: To search for required tools
makenucseq, wordcount, banana, dan
primersearch, showorf
Rasmol
Demo: Rasmol Installation, Insulin Structure.
Alpha helix, Beta strands
Rasmol>rotate y 45
Rasmol>zoom 300
Rasmol>translate x 10
show sequence
show information
Rasmol continued..
Rasmol>select sulphur
Rasmol>colour yellow
Rasmol>cpk
Rasmol>reset
select polar, basic, hydrophobic, acidic, basic
Rasmol Tutorial
clustalx
Used for Multiple sequence alignment
Demo: Installation, phylogenetic tree generation
Demo: NJplot to view phylogenetic tree files
JaMBW
Java based Molecular Biologist's Workbench
A BioSeq File Format Converter
Reverse, Complement, Inverse, Shuffle, Translate
Isoelectric point, Antigenicity index, ORF detection, Dotplot
Finding patterns, restriction sites, binding sites
Primer design, Genome mapping calculators, Buffer calculator
Other Intresting Online Tools
Discovery Engine: www.bioask.com
BioAsk screenshots of upcoming version
Tool to generate Plasmid Map: Savvy
Sequence Analysis: Sewer
Sequence Extractor: Seqext
Thanks for your time
[any material that should appear in print but not on the slide]