We describe two novel sequence similarity search algorithms, FASTS and FASTF, that use multiple short peptide sequences to identify homologous sequences in protein or DNA databases. FASTS searches with peptide sequences of unknown order, as obtained by mass spectrometry-based sequencing, evaluating all possible arrangements of the peptides. FASTF searches with mixed peptide sequences, as genera...

We describe two novel sequence similarity search algorithms, FASTS and FASTF, that use multiple short peptide sequences to identify homologous sequences in protein or DNA databases. FASTS searches with peptide sequences of unknown order, as obtained by mass spectrometry-based sequencing, evaluating all possible arrangements of the peptides. FASTF searches with mixed peptide sequences, as genera...

Motivation: 30 end processing is important for transcription termination, mRNA stability and regulation of gene expression. To identify 30 ends, most techniques use an oligo-dT primer to construct deep sequencing libraries. However, this approach can lead to identification of artifactual polyadenylation sites due to internal priming in homopolymeric stretches of adenines. Although heuristic fil...

Firewall ACLs can contain inconsistencies. There is an inconsistency if different actions can be taken on the same flow of traffic, depending on the ordering of the rules. Inconsistent rules should be notified to the system administrator in order to remove them. Minimal diagnosis and characterization of inconsistencies is a combinatorial problem. Although many algorithms have been proposed to s...

We consider here the problem of Chinese named entity (NE) identification using statistical language model(LM). In this research, word segmentation and NE identification have been integrated into a unified framework that consists of several class-based language models. We also adopt a hierarchical structure for one of the LMs so that the nested entities in organization names can be identified. T...

We consider here the problem of Chinese named entity (NE) identification using statistical language model(LM). In this research, word segmentation and NE identification have been integrated into a unified framework that consists of several class-based language models. We also adopt a hierarchical structure for one of the LMs so that the nested entities in organization names can be identified. T...

To explain agent-identification behaviours, universalist theories in the biological and cognitive sciences have posited mental mechanisms thought to be universal to all humans, such as agent detection and face recognition mechanisms. These universalist theories have paid little attention to how particular sociocultural or historical contexts interact with the psychobiological processes of agent...

this paper addresses a reliable facility location problem with considering facility capacity constraints. in reliable facility location problem some facilities may become unavailable from time to time. if a facility fails, its clients should refer to other facilities by paying the cost of retransfer to these facilities. hence, the fail of facilities leads to disruptions in facility location dec...