My Software
- HMM-FRAME
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HMM-FRAME is designed to accurately locate and correct frameshift errors in next-generation
sequencing (NGS) data using an augmented Viterbi algorithm on profile hidden Markov models (profile HMMs).
By correcting the frameshift errors, it can classify more NGS sequences into their native protein domain families.
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- SAT-Assembler
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SAT-Assembler is a scalable and accurate gene assembly tool for large-scale RNA-Seq and metagenomic data.
It recovers genes from gene families of particular interest to biologists
with high coverage, low chimera rate, and extremely low memory usage compared with exiting gene assembly tools.
Moreover, it is naturally compatible with parallel computing platforms.
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- SALT
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SALT is designed to sensitively and accurately classify short sequences into their native protein
domain families with extremely low memory usage.
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- MetaDomain
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MetaDomain is a protein domain classification tool designed for very short next-generation sequencing reads.
It achieves better sensitivity and low false positive rate compared with the state-of-the-art profile hidden
Markov model (profile HMM) alignment tool in identifying encoded domains from short sequences.
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- PseudoDomain
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Pseudogenes are dysfunctional DNA sequences that share sequence similarities with functional genes.
Accurate identiļ¬cation of pseudogenes is important to understand biological and evolutionary histories
of genomes and genes. PseudoDomain is a processed pseudogene identification tool with high sensitivity and low false positive rate.
It can identify pseudogenes in species that do not have accurate genome annotations.
In addition, it can accurately predict the number and positions of frameshifts within putative pseudogenes.
(SourceForge)
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