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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: pbv@physics.unipune.ernet.in

University of Pune

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.

0.539Pufferfish

0.398Ch. Hamster

0.408Sq. Monkey

0.396Chimp

0.392Dog

0.421Cat

0.48Zebrafish

0.394Pig

0.428Chick

0.418Hamster

0.412Rabbit

0.451Mouse

0.392Human

0.444Rat

GC content indexSpecies

Table 2. Summary of the Codon analysis for Caspase 3 DNA sequences—output from ISHAN.

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.

Human Mouse Rat Dog Chimp Human 100 Mouse 86.5 100 Rat 47.2 51.3 100 Dog 90.3 86.2 47 100 Chimp 88.6 76.4 48.3 79.8 100

Table 3 Summary of Pairwise Alignment (PA) outputs of ISHAN for NFkB p105 AA sequences.

N.B: Numbers represent the Identity (%) among the sequences

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

Table 4: Summary of phylogenetic analysis for various proteins using ISHAN

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

University of Pune