Computational methods for predicting genomic islands in microbial genomes
Clusters of genes acquired by lateral gene transfer in microbial genomes, are broadly referred to as genomic islands (GIs). GIs often carry genes important for genome evolution and adaptation to niches, such as genes involved in pathogenesis and antibiotic resistance. Therefore, GI prediction has gr...
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doaj-cc9e45afbd074079a3541398076556fc2020-11-24T22:31:51ZengElsevierComputational and Structural Biotechnology Journal2001-03702016-01-0114C20020610.1016/j.csbj.2016.05.001Computational methods for predicting genomic islands in microbial genomesBingxin LuHon Wai LeongClusters of genes acquired by lateral gene transfer in microbial genomes, are broadly referred to as genomic islands (GIs). GIs often carry genes important for genome evolution and adaptation to niches, such as genes involved in pathogenesis and antibiotic resistance. Therefore, GI prediction has gradually become an important part of microbial genome analysis. Despite inherent difficulties in identifying GIs, many computational methods have been developed and show good performance. In this mini-review, we first summarize the general challenges in predicting GIs. Then we group existing GI detection methods by their input, briefly describe representative methods in each group, and discuss their advantages as well as limitations. Finally, we look into the potential improvements for better GI prediction.http://www.sciencedirect.com/science/article/pii/S2001037016300046Pathogenicity islandsSequence compositionGenome segmentationComparative genomicsOutlier detection |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Bingxin Lu Hon Wai Leong |
spellingShingle |
Bingxin Lu Hon Wai Leong Computational methods for predicting genomic islands in microbial genomes Computational and Structural Biotechnology Journal Pathogenicity islands Sequence composition Genome segmentation Comparative genomics Outlier detection |
author_facet |
Bingxin Lu Hon Wai Leong |
author_sort |
Bingxin Lu |
title |
Computational methods for predicting genomic islands in microbial genomes |
title_short |
Computational methods for predicting genomic islands in microbial genomes |
title_full |
Computational methods for predicting genomic islands in microbial genomes |
title_fullStr |
Computational methods for predicting genomic islands in microbial genomes |
title_full_unstemmed |
Computational methods for predicting genomic islands in microbial genomes |
title_sort |
computational methods for predicting genomic islands in microbial genomes |
publisher |
Elsevier |
series |
Computational and Structural Biotechnology Journal |
issn |
2001-0370 |
publishDate |
2016-01-01 |
description |
Clusters of genes acquired by lateral gene transfer in microbial genomes, are broadly referred to as genomic islands (GIs). GIs often carry genes important for genome evolution and adaptation to niches, such as genes involved in pathogenesis and antibiotic resistance. Therefore, GI prediction has gradually become an important part of microbial genome analysis. Despite inherent difficulties in identifying GIs, many computational methods have been developed and show good performance. In this mini-review, we first summarize the general challenges in predicting GIs. Then we group existing GI detection methods by their input, briefly describe representative methods in each group, and discuss their advantages as well as limitations. Finally, we look into the potential improvements for better GI prediction. |
topic |
Pathogenicity islands Sequence composition Genome segmentation Comparative genomics Outlier detection |
url |
http://www.sciencedirect.com/science/article/pii/S2001037016300046 |
work_keys_str_mv |
AT bingxinlu computationalmethodsforpredictinggenomicislandsinmicrobialgenomes AT honwaileong computationalmethodsforpredictinggenomicislandsinmicrobialgenomes |
_version_ |
1725735936403177472 |