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Bioinformatics Tool Developed

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Bioinformatics Tool Developed

Bioinformatics Tool Developed

  • Shekhawat, S. S., Vijaya Kumar S., Das A (2007). EGF – LD Finder for identification of EGF like domains. (EGF LD Finder). 

    Summary:

    EGF-like domains are found in a variety of proteins and are usually implicated in protein-protein interactions. EGF-like domains can be categorized into 3 types TYPE-I, TYPE-II and TYPE-III EGF domains based upon their structure and function. EGF like Domains Analysis & Comparison Package is a web based Bioinformatic tool that can analyze the given sequence and predict if it contains EGF-like domains. Given a Sequence in any format, it would search for EGF type domains in it and also specify the positions of these domains if any. The tool is GUI based and has been developed using JAVA Applet Programming. EGF like Domains Analysis & Comparison Package also shows the relative graphical positioning of these domains and one can query for the sequences of these domains. The tool also consists of an EGF library, which has about 200 different sequences that contain EGF domains in them. The program uses basic Bioinformatic searching algorithm technique to match to a particular given sequence. It first searches for a set of six Cysteines in the sequence and passes it on for further analysis. Once a set of six Cysteines has been identified, the program looks for whether the given part of the sequence matches to Type-I, Type-II or Type-III domain, based on weight given to each type of domain. As the sequence is matched to each of the Types, a count is increased for each of them. The matching is first carried out on the basis of sequence and then based on the gaps between each of the Cysteines in each of the Domain Types. Once a residue is matched to the set standards the count is increased and once it does not match the count is decreased and so on for each of the domain. Finally all three counts are compared and the Type of Domain identified. If all the counts are too low to be compared then the result is ‘NO EGF like Sequences Found’.

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