Wise2.4

Wise2.4 implements GeneWise and Genomewise algorithms to integrate gene prediction with homology searches by aligning protein sequences or protein Hidden Markov Models (HMMs) to genomic DNA to predict gene structures while accounting for introns and frameshifting errors.

Key Features:

• Gene prediction with homology integration: Integrates gene prediction with homology searches to analyze genomic DNA in relation to protein sequences or protein HMMs.
• Protein and HMM alignment: Aligns protein sequences and protein Hidden Markov Models (HMMs) to genomic DNA for structure inference.
• Intron modeling: Accounts for introns in genomic alignments to predict spliced gene structures.
• Frameshift handling: Models frameshifting errors within coding regions during alignment and prediction.
• HMM-derived approach: Operates on principles derived from hidden Markov models (HMMs).
• cDNA and EST parsing: Parses cDNA- and EST-defined spliced structures to support annotation.
• Genomewise final parse: Provides a Genomewise algorithm that performs a final parse of gene structure across defined splicing patterns.
• Ensembl integration: Algorithms are used as integral components of the Ensembl annotation system.

Scientific Applications:

• Genome annotation and gene prediction: Predicts gene structures and annotates genomic regions by comparing DNA to protein sequences or protein HMMs.
• Drosophila melanogaster assessment: Was applied to a 2.9-Mb region of Drosophila melanogaster in the Genome Annotation Assessment Project (GASP).
• Complex locus analysis: Applied to loci complicated by transposons, pseudogenes, or annotation oversights, with these factors noted as sources of inaccuracy.
• Splice-aware annotation using cDNA/EST evidence: Provides accurate and complete gene annotations when cDNA or EST spliced evidence is available.

Methodology:

Uses HMM-derived algorithms to align protein sequences or protein HMMs to genomic DNA, modeling introns and frameshifting errors and parsing cDNA- and EST-defined spliced structures, with Genomewise performing a final parse across defined splicing patterns.