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View Code? Open in Web Editor NEWLocal Alignment Search for Strings, BLAST like string searching algorithm. Final Year Project. B.Tech NIT Silchar
Local Alignment Search for Strings, BLAST like string searching algorithm. Final Year Project. B.Tech NIT Silchar
This is a sub issue of #4
Task:
Traverse the database, and keep calculating the score of k length subsequences till
the score of k length subsequence matches the score of LSS.
This is the sub issue of #4
Task:
Calculate score of each seed
Hash the input file such that count of each character is maintained in an array or a HashMap.
Change fixed seed length such that user can give it from command line. If not given by user then it should take seed length = 3.
i.e.,
Seed Length = s = args[4] or 3
Maintain a count of occurrences of all characters with respect to each other.
This is a sub issue of issue #4
Task :
Using the search pattern create the k length seeds. If pattern length is of m length then m-k+1 seeds will be generated.
This is a subissue of #4
Task:
Identify the least scoring seeds (LSS)
Naming conventions used in the algorithm are as follows :-
โข w - Query string.
โข wi - Seeds.
โข k - Size of a seed.
โข D - Database.
โข T - Threshold.
Related Issues will tag this issue in their description!
This issue is a sub issue of #4.
Task :
Read scoring matrix stored in a text file.
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