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In this project, our aim is to query CODIS primer sequences within the human genome. CODIS, or the Combined DNA Index System, is a program in the United States utilized for law enforcement purposes, aiding in crime-solving by identifying and linking DNA evidence. Forensic laboratories contribute and compare DNA profiles electronically at various levels: the Local DNA Index System (LDIS), the State DNA Index System (SDIS), and the National DNA Index System (NDIS). We will be conducting BLAST+ searches with CODIS primer sequences against several human genomic sequences, including the human reference genome, a Caucasian individual for the Ashkenazi Human Reference Genome project, and a female Sumatran orangutan. With the virtual PCR amplicons, we will proceed to create a multiple sequence alignment and generate a guide tree. The guide tree is computed from the distance matrix generated from pairwise alignment scores. We are going to use Clustal Omega to perform the alignment and NJplot to visualize the resulting phylogenetic tree. All files from this chapter are available from the book’s GitHub repository at CompBiol3/18_PrimerBlast .

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BLASTing Forensic PCR Primers

  • 章节

  • 发表日期：

    2025年

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  • Röbbe Wünschiers

摘要

In this project, our aim is to query CODIS primer sequences within the human genome. CODIS, or the Combined DNA Index System, is a program in the United States utilized for law enforcement purposes, aiding in crime-solving by identifying and linking DNA evidence. Forensic laboratories contribute and compare DNA profiles electronically at various levels: the Local DNA Index System (LDIS), the State DNA Index System (SDIS), and the National DNA Index System (NDIS). We will be conducting BLAST+ searches with CODIS primer sequences against several human genomic sequences, including the human reference genome, a Caucasian individual for the Ashkenazi Human Reference Genome project, and a female Sumatran orangutan. With the virtual PCR amplicons, we will proceed to create a multiple sequence alignment and generate a guide tree. The guide tree is computed from the distance matrix generated from pairwise alignment scores. We are going to use Clustal Omega to perform the alignment and NJplot to visualize the resulting phylogenetic tree. All files from this chapter are available from the book’s GitHub repository at CompBiol3/18_PrimerBlast .