A discriminative method for remote homology detection based on n-peptide compositions with reduced amino acid alphabets

Ogul, Hasan; Mumcuoglu, E.U.

doi:10.1016/j.biosystems.2006.03.006

Cited by 33 publications

(17 citation statements)

References 18 publications

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“…Together with the measurement based on k-mer distance, the construction of the phylogenetic trees could even speed up for more than three orders of magnitude. Similar results are also observed in other studies [147]. The efficiency gain could also be reached in experimental designs [148,149].…”

Section: Implications Of Simplified Amino Acid Alphabetssupporting

confidence: 90%

Simplification of complexity in protein molecular systems by grouping amino acids: a view from physics

Wang

2016

Advances in Physics: X

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Section: Implications Of Simplified Amino Acid Alphabetssupporting

confidence: 90%

Simplification of complexity in protein molecular systems by grouping amino acids: a view from physics

Wang

2016

Advances in Physics: X

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“…LSA [24] improved the performance of building-block-based methods. SVM-N-Peptide [25] reduced the size of amino acid alphabet for increasing values of k . The performance of the sequence-based methods is not satisfying because these methods only use the sequence features without using the evolutionary information or 3-dimension structure.…”

Section: Introductionmentioning

confidence: 99%

Effects of error-correction of heterozygous next-generation sequencing data

et al. 2014

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BackgroundError correction is an important step in increasing the quality of next-generation sequencing data for downstream analysis and use. Polymorphic datasets are a challenge for many bioinformatic software packages that are designed for or assume homozygosity of an input dataset. This assumption ignores the true genomic composition of many organisms that are diploid or polyploid. In this survey, two different error correction packages, Quake and ECHO, are examined to see how they perform on next-generation sequence data from heterozygous genomes.ResultsQuake and ECHO perform well and were able to correct many errors found within the data. However, errors that occur at heterozygous positions had unique trends. Errors at these positions were sometimes corrected incorrectly, introducing errors into the dataset with the possibility of creating a chimeric read. Quake was much less likely to create chimeric reads. Quake's read trimming removed a large portion of the original data and often left reads with few heterozygous markers. ECHO resulted in more chimeric reads and introduced more errors than Quake but preserved heterozygous markers.Using real E. coli sequencing data and their assemblies after error correction, the assembly statistics improved. It was also found that segregating reads by haplotype can improve the quality of an assembly.ConclusionsThese findings suggest that Quake and ECHO both have strengths and weaknesses when applied to heterozygous data. With the increased interest in haplotype specific analysis, new tools that are designed to be haplotype-aware are necessary that do not have the weaknesses of Quake and ECHO.

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“…Recent studies showed that the reduced alphabet scheme can improve the performance and reduce the computational cost of some predictors for protein remote homology detection, fold recognition, protein disordered region prediction [74], [94], [95], etc. In this section, we investigated whether the predictive performance and computational cost of iDNA-Prot|dis can be further improved by employing the reduced alphabet scheme.…”

Section: Resultsmentioning

confidence: 99%

iDNA-Prot|dis: Identifying DNA-Binding Proteins by Incorporating Amino Acid Distance-Pairs and Reduced Alphabet Profile into the General Pseudo Amino Acid Composition

et al. 2014

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Playing crucial roles in various cellular processes, such as recognition of specific nucleotide sequences, regulation of transcription, and regulation of gene expression, DNA-binding proteins are essential ingredients for both eukaryotic and prokaryotic proteomes. With the avalanche of protein sequences generated in the postgenomic age, it is a critical challenge to develop automated methods for accurate and rapidly identifying DNA-binding proteins based on their sequence information alone. Here, a novel predictor, called “iDNA-Prot|dis”, was established by incorporating the amino acid distance-pair coupling information and the amino acid reduced alphabet profile into the general pseudo amino acid composition (PseAAC) vector. The former can capture the characteristics of DNA-binding proteins so as to enhance its prediction quality, while the latter can reduce the dimension of PseAAC vector so as to speed up its prediction process. It was observed by the rigorous jackknife and independent dataset tests that the new predictor outperformed the existing predictors for the same purpose. As a user-friendly web-server, iDNA-Prot|dis is accessible to the public at http://bioinformatics.hitsz.edu.cn/iDNA-Prot_dis/. Moreover, for the convenience of the vast majority of experimental scientists, a step-by-step protocol guide is provided on how to use the web-server to get their desired results without the need to follow the complicated mathematic equations that are presented in this paper just for the integrity of its developing process. It is anticipated that the iDNA-Prot|dis predictor may become a useful high throughput tool for large-scale analysis of DNA-binding proteins, or at the very least, play a complementary role to the existing predictors in this regard.

show abstract

A discriminative method for remote homology detection based on n-peptide compositions with reduced amino acid alphabets

Cited by 33 publications

References 18 publications

Simplification of complexity in protein molecular systems by grouping amino acids: a view from physics

Simplification of complexity in protein molecular systems by grouping amino acids: a view from physics

Effects of error-correction of heterozygous next-generation sequencing data

iDNA-Prot|dis: Identifying DNA-Binding Proteins by Incorporating Amino Acid Distance-Pairs and Reduced Alphabet Profile into the General Pseudo Amino Acid Composition

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