ArticleNucleic acids research2008
Genome bias influences amino acid choices: analysis of amino acid substitution and re-compilation of substitution matrices exclusive to an AT-biased genome.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 31 citations in OpenAlex.
- Identification of a nuclear localization signal in the Plasmodium falciparum CTP: phosphocholine cytidylyltransferase enzyme.Scientific reports · 2020Article
- Substitution scoring matrices for proteins - An overview.Protein science : a publication of the Protein Society · 2020Review
- Uracil moieties inFEBS open bio · 2018Article
- GC bias lead to increased small amino acids and random coils of proteins in cold-water fishes.BMC genomics · 2018Article
- Article
- Expansion of Lysine-rich Repeats in Plasmodium Proteins Generates Novel Localization Sequences That Target the Periphery of the Host Erythrocyte.The Journal of biological chemistry · 2016Article
- ALP & FALP: C++ libraries for pairwise local alignment E-values.Bioinformatics (Oxford, England) · 2016Article
- From local structure to a global framework: recognition of protein folds.Journal of the Royal Society, Interface · 2014Review
- The parasite specific substitution matrices improve the annotation of apicomplexan proteins.BMC genomics · 2012Article
- Local structural differences in homologous proteins: specificities in different SCOP classes.PloS one · 2012Article
- ApicoAlign: an alignment and sequence search tool for apicomplexan proteins.BMC genomics · 2011Article
- A novel substitution matrix fitted to the compositional bias in Mollicutes improves the prediction of homologous relationships.BMC bioinformatics · 2011Article
- Proteomic analysis revealed alterations of theResearch and reports in tropical medicine · 2011Article
- A genome alignment algorithm based on compression.BMC bioinformatics · 2010Article
- Revisiting the Plasmodium falciparum RIFIN family: from comparative genomics to 3D-model prediction.BMC genomics · 2009Article
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3 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
The genomic era has seen a remarkable increase in the number of genomes being sequenced and annotated. Nonetheless, annotation remains a serious challenge for compositionally biased genomes. For the preliminary annotation, popular nucleotide and protein comparison methods such as BLAST are widely employed. These methods make use of matrices to score alignments such as the amino acid substitution matrices. Since a nucleotide bias leads to an overall bias in the amino acid composition of proteins, it is possible that a genome with nucleotide bias may have introduced atypical amino acid substitutions in its proteome. Consequently, standard matrices fail to perform well in sequence analysis of these genomes. To address this issue, we examined the amino acid substitution in the AT-rich genome of Plasmodium falciparum, chosen as a reference and reconstituted a substitution matrix in the genome's context. The matrix was used to generate protein sequence alignments for the parasite proteins that improved across the functional regions. We attribute this to the consistency that may have been achieved amid the target and background frequencies calculated exclusively in our study. This study has important implications on annotation of proteins that are of experimental interest but give poor sequence alignments with standard conventional matrices.
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