Poster Title

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

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).

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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).