Background: Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs) are one of the most successful approaches in addre...
1 Profile Hidden Markov Models (profile HMMs) are used as a popular bioinformatics tool for sensitive database searching, e.g. a set of not annotated protein sequences is compared...
Motivation: Non-coding RNAs (ncRNAs)--functional RNA molecules not coding for proteins--are grouped into hundreds of families of homologs. To find new members of an ncRNA gene fam...
One key element in understanding the molecular machinery of the cell is to understand the meaning, or function, of each protein encoded in the genome. A very successful means of i...
Background: Most profile and motif databases strive to classify protein sequences into a broad spectrum of protein families. The next step of such database studies should include ...