Transcript - Department of Physics

University of Pune
WELCOME
to
Integrated Software for Homology Analysis (ISHAN)
Results page
ISHAN formulated by :
Biophysics Laboratory,
Department of Physics, University of Pune,
Pune 411 007 INDIA.
Ownership: Prof P.B. Vidyasagar, Mr. Pratip Shil, Mr. Niraj Dudani
Contact: [email protected]
Figure 1a: Graphical User Interface of ISHAN- form for submission of query
set
Figure 1b: Graphical User Interface of ISHAN - choosing the parameters
Figure 2a: Results from ISHAN as HTML page – list of sequences
Figure 2b: Results from ISHAN as HTML page – Table summarizing the
identities (%)
Figure 3: The Phylogenetic tree for Caspase 3 DNA sequences - output
of ISHAN, which utilizes PHYLIP package for the Phylogenetic analysis
Figure 4: The Phylogenetic tree for NF kB p105 AA sequences from
mammalian species - output of ISHAN.
Table 1: Identity (%) among the Caspase 3 DNA sequences; summary of Pairwise Alignment
(PA) outputs of ISHAN in tabulated form. ALIGN tool was chosen by user for the comparison
of pairs of sequences (all possible combinations). ISHAN has provisions for generating similar
table whenever a set of sequences are tested for PA.
Table 2. Summary of the Codon analysis for Caspase 3 DNA sequences—
output from ISHAN.
Species
GC content index
Rat
0.444
Human
0.392
Mouse
0.451
Rabbit
0.412
Hamster
0.418
Chick
0.428
Pig
0.394
Zebrafish
0.48
Cat
0.421
Dog
0.392
Chimp
0.396
Sq. Monkey
0.408
Ch. Hamster
0.398
Pufferfish
0.539
N.B.: GC content index gives the proportion of the sequence composed of Guanine–Cytosine. Max
value of GC content index = 1.00 corresponds to 100% of the sequence being composed of GC.
Table 3 Summary of Pairwise Alignment (PA) outputs of ISHAN for NFkB p105
AA sequences.
Human
Mouse
Rat
Dog
Chimp
Human
100
86.5
47.2
90.3
88.6
Mouse
100
51.3
86.2
76.4
Rat
100
47
48.3
Dog
100
79.8
Chimp
100
N.B: Numbers represent the Identity (%) among the sequences
Table 4: Summary of phylogenetic analysis for various proteins using ISHAN
Sequence
Species closest to Homo sapiens
Number of
sequences in
query set
Bcl2 DNA
Felis catus (Cat) (91%)
5
Caspase 1 DNA
Sus scrofa (Pig) (80.2%)
6
Caspase 3 DNA
Pan troglodytes (Chimpanzee) (99.5%)
14
NFkB – p 105 DNA
Canis familiaris (Dog) (88.7%)
5
Bcl2 AA
Felis catus (Cat) (90.8%)
7
Caspase 1 AA
Sus scrofa (Pig) (72.5%)
10
Caspase 2 AA
Mus musculus (Mouse) (91%)
5
Caspase 3 AA
Pan troglodytes (Chimpanzee) (99.3%)
9
Caspase 6 AA
Mus musculus (Mouse) (84.7%)
5
NFkB - p 100 AA
Mus musculus (Mouse) (91.9%)
6
NFkB - p 105 AA
Canis familiaris (Dog) (88.6%)
5
University of Pune
To try ISHAN please visit:
http://physics.unipune.ernet.in/~pbv/ishan.html
Please Note:
ISHAN can be downloaded freely and requires Windows XP. To install
and run ISHAN in your PC please install Java Runtime Environment
version 1.4 or later.
Biophysics Laboratory , Department of Physics, University of Pune, Pune 411007 INDIA