researches

1. "Diversity analysis of fish through bioinformatics tools",
Susmita Sarkar, A.D.Upadhyay and A.K. Roy Bioinformatics Centre, College of Fisheries, CAU Lembucherra, Tripura

Abstract: Bioinformatics is an application of computational technology for the management of biological information. The evolution of bioinformatics started with sequence analysis which led to high-through put whole genome analysis and transcriptome annotation. Further due to increase in high-performance computing technologies, sophisticated algorithms and advanced data management capabilities leading to increase its application. In this study an attempt has been made for diversity analysis of fish through bioinformatics tools. For BLAST and multiple sequence alignment analysis, 10 protein sequences were downloaded from the NCBI database. These sequences are: cytocrome c oxidase and cytocrome b oxidase from Rohu and Catla fish and another one sequence, CIRMR vasa protein (fragment) from mouse (out group sequence). After phylogram analysis it was found that these sequences formed 3 major clusters including 5 minor clusters. It was further observed that a total of 5 sequences in major cluster- I,which belong to cytocrome b oxidase protein in Rohu and Catla fish ; major cluster –II, related to cytocrome c oxidase in Catla and Rohu comprises four sequences and lastly major cluster- III was formed as outer group sequences for CIRMR vasa protein (fragment)from mouse. In the present analysis it is shown that these cluster finally happen when more than 90% similarity were detected between protein sequences whereas outer group cluster shows only about 7% similarity. Thus the present study determines major hierarchical clustering formed in fish protein gene sequences and also gathers knowledge of sequence similarity in fish genome analysis.

2. "Analysis of some Bony Fish Gene Sequence Using CLUSTAL Omega",
Susmita Sarkar, A.D.Upadhyay and A.K. Roy Bioinformatics Centre, College of Fisheries, CAU Lembucherra, Tripura

Abstract: A tool that simultaneously aligns multiple nucleotide sequences, automatically utilizes information about nucleotide a good compromise between speed and accuracy will have practical advantages. In this study mitochondrial DNA and cytocrome oxidase subunit 1gene was analysed for evolutionary relationship by using CLUSTAL omega. In this study BLAST and multiple sequence alignment was done on Amblyceps mangois 4 gene sequences, Mola mola 3gene sequences, Bagarious yarrelli 3 gene sequences, Barilious barna 3 gene sequences and Chanda nama 3 gene sequences downloading from NCBI database. There are sixteen fresh water bony fish gene sequences BLASTn shows only few species in most primitive category provide lineage for other species evolution. In phylogenetic analysis of fish gene it was found that five cluster were formed. In major Cluster-I formed in Amblyceps mangois 4 gene sequence with99.01-100% similarity, major cluster-II are formed in Mola mola 3gene sequence with 98.77-100% similarity. Major cluster-III is formed in Bagarious yarrelli 3 gene sequences with 100% similarity. Major cluster-IV are formed in Barilious barna 3 gene sequence with 98-100 %similarity and lastly cluster-V are formed Chanda nama 3 gene sequence with 99-100 % similarity. These, Result shows when the rate of evolution varies extensively from branch to branch, many methods fail to do these clustering of gene sequence. The CLUSTAL omega alignment all nucleotide sequence in a line and phylogram show evolutionary relationship between all species by comparing the all sixteen fresh water fish gene. Results show that CLUSTAL omega has reasonable runtime performance and alignment accuracy which can be a tool for a broad range of problems of phylogenetic analysis.