Protocol for using NoBadWordsCombiner to merge and minimize "bad words" from BLAST hits against multiple eukaryotic gene annotation databases

Xi Zhang; Yining Hu; David Roy Smith

doi:10.1016/j.xpro.2021.100888

Protocol for using NoBadWordsCombiner to merge and minimize "bad words" from BLAST hits against multiple eukaryotic gene annotation databases

STAR Protoc. 2021 Oct 16;2(4):100888. doi: 10.1016/j.xpro.2021.100888. eCollection 2021 Dec 17.

Authors

Xi Zhang^{1

2}, Yining Hu³, David Roy Smith⁴

Affiliations

¹ Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
² Institute for Comparative Genomics, Dalhousie University, Halifax, NS B3H 4R2, Canada.
³ Department of Computer Science, Western University, London, ON N6A 5B7, Canada.
⁴ Department of Biology, Western University, London, ON N6A 5B7, Canada.

Abstract

Annotating protein-coding genes can be challenging, especially when searching for the best hits against multiple functional databases. This is partly because of "bad words" appearing as top hits, such as hypothetical or uncharacterized proteins. To help alleviate some of these issues, we designed a bioinformatics tool called NoBadWordsCombiner, which efficiently merges the hits from various databases, strengthening gene definitions by minimizing functional descriptions containing "bad words." Unlike other available tools, NoBadWordsCombiner is user friendly, but it does require users to have some general bioinformatics skills, including a basic understanding of the BLAST package and dash shell in Linux/Unix environments. For complete details on the use and execution of this protocol, please refer to Zhang et al. (2021a).

Keywords: Bioinformatics; Genomics; Sequence analysis.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Computational Biology / methods*
Databases, Genetic*
Humans
Mice
Molecular Sequence Annotation* / methods
Proteins / genetics
Sequence Alignment / methods*
Software*

Substances

Proteins