BLAST redundancy cleaner: a bioinformatics tool that allows for easy viewing of complex genomic repeat BLAST results
Grade Level at Time of Presentation
Freshmen
Major
Agricultural and Medical Biotechnology; Biology
Minor
Computer Science
2nd Grade Level at Time of Presentation
Junior
2nd Student Major
Agricultural and Medical Biotechnology
2nd Student Minor
Computer Science
3rd Grade Level at Time of Presentation
Senior
3rd Student Major
Biology
4th Grade Level at Time of Presentation
Senior
4th Student Major
Biology
Institution
University of Kentucky
KY House District #
75
KY Senate District #
13
Faculty Advisor/ Mentor
Dr. Mark Farman; Dr. Mostafa Rahnama; Dr. Jerzy W. Jaromczyk; Dr. Patrick Calie
Department
Dept. of Computer Science
Abstract
Most presently characterized genomic repeat elements contain internal repeat sequences, causing bioinformatics program like BLAST to return redundant hits. To combat this problem, we have developed BLASTrec: a command-line tool implemented in Python v3+ that can flexibly clean BLAST reports to remove redundancy. Results are returned in in file formats that allow for easy and compact viewing in visualizers such as IGV. BLASTrec tool supports an assortment of options that control the cleanliness of the final output, final output filetypes, and provide the ability to run BLASTn-short in addition to BLASTn. Furthermore, BLASTrec can be used in a wide variety of genomic studies, including characterizing the movement of known genomic repeat elements and identifying potential novel repeat elements through genome self-comparison. This works is a part of the NSF project to investigate telomere roles in fungal genome evolution: Dr. Mark Farman (PI).
BLAST redundancy cleaner: a bioinformatics tool that allows for easy viewing of complex genomic repeat BLAST results
Most presently characterized genomic repeat elements contain internal repeat sequences, causing bioinformatics program like BLAST to return redundant hits. To combat this problem, we have developed BLASTrec: a command-line tool implemented in Python v3+ that can flexibly clean BLAST reports to remove redundancy. Results are returned in in file formats that allow for easy and compact viewing in visualizers such as IGV. BLASTrec tool supports an assortment of options that control the cleanliness of the final output, final output filetypes, and provide the ability to run BLASTn-short in addition to BLASTn. Furthermore, BLASTrec can be used in a wide variety of genomic studies, including characterizing the movement of known genomic repeat elements and identifying potential novel repeat elements through genome self-comparison. This works is a part of the NSF project to investigate telomere roles in fungal genome evolution: Dr. Mark Farman (PI).