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RAJESH KUMAR
Ph.D 1st yr
Dairy Microbiology Division
N.D.R.I
Introduction
Bio-informatics/Computational Biology:-
gene finding.
genome assembly.
modeling of evolution.
Sequence Analysis
Analysis
Phylogenetic Tree
Comparative Genomics
Shotgun Sequencing
Computer programs
Sequence Alignment:-
arrangement of two or more sequences & highlighting
their similarity.
tcctctgcctctgccatcat---caaccccaaagt
|||| ||| ||||| ||||| ||||||||||||
tcctgtgcatctgcaatcatgggcaaccccaaagt
Structural Alignment
Multiple Alignment
Programs
Clustal is used in cladistics to build phylogenetic trees
Framesearch
Software:-
Ssearch
Where does the DNA that I've just sequenced come from?
FASTA:-
protein:protein
DNA:DNA.
Protein:translated DNA
Ordered or unordered peptide searches.
EMBOSS
MUMmer 3.0
Open source.
Improved efficiency.
Applications:-
WoLF PSORT
WoLF PSORT Prediction
PSORT II (Recommended for animal/yeast sequences)
PSORT II Users' Manual
PSORT II Prediction
PSORT (Old version; for bacterial/plant sequences)
PSORT-B (Recommended for Gram-negative bacteria)
PSORT-B Prediction
PSORT-B, a program applicable to the sequences of Gram-negative
bacteria.
PSORT Prediction
Source of Input Sequence:
Gram-positive bacterium
Gram-negative bacterium
yeast
animal
plant
Enter your Amino Acid sequence below (by copy & paste):
restriction analysis
amino acids analysis
multiple sequence alignment tool
dot plot
calculation of molecular weights and chemical properties of proteins
prediction of 3D structures for small amino acids sequences.
UniPro DPview
This is a tool for finding and analyzing matches between
genomes.
SEQtools
Program package for routine handling and analysis of DNA
and protein sequences.
The package includes general facilities for sequence and
contig editing, restriction enzyme mapping, translation, and
repeat identification.
DNA Club
DNA analysis software,
Features:- remove vector sequence, find ORF, sequence
editing, translate to protein sequence, protein sequence
editing, RE Map, RE Map with translation, PCR primer
selection, primer or probe evaluation.
ZCURVE
New highly accurate system for recognizing protein coding
genes in bacterial and archaeal genomes based on the Z
curve theory of DNA sequence.
Drawbacks:-
labor-intensive, time-consuming, and costly.
Single-locus sequence typing(SLST)
The genetic alterations in SSR regions include both point mutations and
intragenic recombination that arise by slipped-strand mispairing during
chromosomal replication and that result in a high degree of
polymorphism.