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I am new in Bioinformatics and recently studying UCLUST algorithm by Robert Edgar(2010). It is a fast sequence searching and clustering algorithm. The algorithm is heuristic based. I studied that first, this algorithm finds unique common words(k-mers) between a query sequence and a target sequence.(one of the sequences from sequence database). If there are enough common k-mers between a target sequence and a database sequence then it is selected for the alignment in the next step, otherwise skipped. All such sequences having enough common k-mers are selected. Target sequences are compared in order of decreasing common k-mers.

In next step, HSPs (High Scoring Segment Pairs) are identified. For this purpose, exact matching words between a query sequence and a target sequence (one of the sequences selected in the previous step) are found. I AM CONFUSED AT THIS POINT. Is it necessary that these matching words(between the query sequence and the target sequence) be at same positions ?

Kindly if some one explains with an example, will be very help full.

Any guidance will highly be appreciated.

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