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Frameshift detection software tools | Genome annotation

Frameshift (FS) prediction is important for analysis and biological interpretation of metagenomic sequences. Since a genomic context of a short metagenomic sequence is rarely known, there is not enough data available to estimate parameters of species-specific statistical models of protein-coding and non-coding regions. Source text: Tang et al., 2013.

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FragGeneScan
A gene prediction method which combines sequencing error models and codon usages in a hidden Markov model to improve the prediction of protein-coding region in short reads. The performance of FragGeneScan was comparable to Glimmer and MetaGene for complete genomes. But for short reads, FragGeneScan consistently outperformed MetaGene (accuracy improved ∼62% for reads of 400 bases with 1% sequencing errors, and ∼18% for short reads of 100 bases that are error free). When applied to metagenomes, FragGeneScan recovered substantially more genes than MetaGene predicted (>90% of the genes identified by homology search), and many novel genes with no homologs in current protein sequence database.
BER / BLAST-Extend-Repraze
Permits the identification of potential frameshifts or point mutations in a given open reading frame (ORF). BER can process precomputed blastp results and can be able to handle both wu-blastp and NCBI blastp. It includes several functionalities allowing the following action: converting raw BLAST output to internal btab format, filtering of btab hits by passed cutoffs, or creating a nucleotide database containing the corresponding nucleotide sequence for each query protein whose hits pass cutoffs.
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