Structure-based Functional Annotation

Sequence- and Structure-Based Functional Annotation

Treebank vs. Xbar-based Automatic F-structure Annotation Treebank vs. Xbar-based Automatic F-structure Annotation

Manual, large scale (computational) grammar development is time consuming, expensive and requires lots of linguistic expertise. More recently, a number of alternatives based on treebank resources (such as Penn-II, Susanne, AP treebank) have been explored. The idea is to automatically \induce" or rather read oo (P)CFG grammars from the parse annotated treebank resources and to use the treebank g...

Comparison of structure-based and threading-based approaches to protein functional annotation.

To exploit the vast amount of sequence information provided by the Genomic revolution, the biological function of these sequences must be identified. As a practical matter, this is often accomplished by functional inference. Purely sequence-based approaches, particularly in the "twilight zone" of low sequence similarity levels, are complicated by many factors. For proteins, structure-based tech...

Literature Based Functional Annotation of Genes

This paper proposes a fast and automatic functional annotation method for hundreds of unannotated genes in biological databases. Genes are often described and discussed in biomedical literature that can be used to unravel the functions of genes. We have proposed a reliable text mining approach to discover functional annotations for genes from literature. This approach was validated by building ...

A protein structure based annotation of genomes

A strategy for protein structure and function based annotation of genomes was developed, evaluated and applied to the proteins of several genomes including the human genome. First the performance of the widely-used homology-based sequence comparison program PSI-BLAST to detect distant homologous relationships (<20% sequence identity) was evaluated. The benchmark is based on two sets of sequence...